OK, I've taken a long route, but narrowed things down to a Nikon D800e based system, a Canon full-frame system, or a Pentax K-5 IIs system. All of them met my needs just fine, although the D800e system gave me better image quality and the Pentax a bit less.
Let's Begin With: Don't Do What I Did
Sometimes the main purpose of my life is simply to serve as a warning to others. By now it should be apparent that I made some major mistakes.
Foremost was that I overreacted. Following my lifelong philosophy of 'Anything worth doing is worth doing to excess' I decided to exit Micro 4/3 when I found it didn't fit all of my needs. Despite the fact that I said, very clearly, when starting this that I knew there was no perfect camera system, even for one individual. The grass will always be greener in some area on the other side of the fence.
In retrospect, it would have made more sense to buy a new camera and lens to fill my major need at 400mm and then decide if I wanted to move entirely. I used a shotgun to kill the fly that was irritating me.
Several people have suggested 400mm options for micro 4/3, though, and I do want to mention that so far there hasn't been a suggestion I haven't tried. They just didn't work for me, But in retrospect, at this point I should be buying a body and couple of lenses, and not have gotten rid of all my Micro 4/3 stuff. Then I could have decided if I wanted to completely migrate or continue with both systems.
Show Me the Money
I spent some time looking at lens combinations I would likely buy, to reevaluate expenses. Camera, macro lens, at least one fast prime, standard zoom, at least one wide aperture prime, a wide-angle zoom, and 400mm equivalent lens were absolute necessities. I had decided to keep my system under $9,000 so a little modification of my initial lists was in order.
The first modification knocked roughly $1,500 from my Canon and Nikon purchase prices. I had initially planned on the Nikon 14-24 f/2.8 because it's the world's best wide zoom and the Canon 16-35 f/2.8 as the closest match. During my evaluation time I had decided I preferred the Canon 14mm f/2.8 to the 16-35mm f/2.8 because it was sharper and because when looking at what I actually shoot it became obvious I use my wide zooms at the widest end almost all of the time.
After realizing I rarely shoot architecture this wide I decided I'd save $1,500 either way and pick up a RokiBowYang 14mm f/2.8 lens. It has more barrel distortion (5.2%) compared to the Nikon (3.9% at 14mm) and the Canon (1.7%) but it has resolution every bit as good as the brand-name lenses. I don't mind manually focusing at this wide angle (truth is I usually set this kind of lens at it's hyperfocal distance and then shoot away). I know, because I've taken them apart, that they aren't going to hold up well, and I know they are about impossible to get repaired. But buying a replacement RokiBowYang costs less than a standard repair on a Nikon 14-24mm, so i almost consider it a disposable lens. This choice, very obviously, might not work for you.
The second modification had to do with camera bodies. On the Canon side I truly waffled about whether I preferred the 5D Mk III's extra pixels and better autofocus or the 6D's built in Wi-Fi, which I really found useful. So I saved $1,100 and went with the 6D. The Nikon decision was tougher. I could save the same $1,100 choosing a D600 instead of a D800. For me, the major attraction, even though I don't absolutely need it, was the big megapixel images. It gives me some flexibility in cropping and even lens selection. So on the Nikon side I decided I'd pay the difference.
Finally, I decided to leave off a 70-200 f/2.8 lens. I don't shoot action sports, and would be fine with the f/4 versions for either Canon or Nikon. The 70-200s tend to be travel / vacation lenses for me, and for right now I'll just rent one for vacation. I may add one in a few months, but might rather prefer 85mm and 135mm primes instead.
When the dust had settled, it was pretty easy to meet my $9,000 budget with any system and I can probably save a few hundred off of the list prices below with some smart shopping.
Nikon D800e $3,097 Canon 6D $2,099 Pentax K5 IIs $1,197
Nikon 300mm f/4 with 1.4x TC $1,879 Canon 400mm f/5.6 $1,339 Pentax 300mm f/4 $1,370
Nikon 105mm f/2.8 VR Micro $899 Canon 100mm f/2.8 IS L $1,049 Pentax 100mm f/2.8 Macro $847
Tamron 24-70mm f/2.8 VC $1,299 Canon 24-70mm f/2.8 Mk II $2,149 Pentax 16-50mm f/2.8 $1,470
Rokinon 14mm f/2.8 $399 Rokinon 14mm f/2.8 $399 Sigma 10-20 f/3.5 $599
Sigma 35mm f/1.4 $899 Sigma 35mm f/1.4 $899 Pentax 31mm f/1.8 $990
TOTAL $8.472 TOTAL $7,934 TOTAL $6,473
Other Things I Considered
Service and Support
I mentioned in the first post that I'm a fanatic about customer service and repairs. That's a big edge to Canon USA compare to Nikon USA right now (it's different in different countries), and right now is when I'm making my decision. Fanboys can go off as much as they want, but I handled several thousand repairs last year. Nikon takes, on average, three times as long at double the cost. (Lensrentals insider joke: What do you call a D800 with a scratched sensor? Parts. Because at $1,800 for a sensor replacement . . . )
I haven't had many Pentax repairs so I looked into their service and got good news and bad. The good was a really nice customer support system with live chat and quick, knowledgeable phone support. The bad news was when I asked how long repair turnaround time would be the answer was 20 to 30 days. So I ranked them between Canon and Nikon.
My Personal Rant
This may not bother you at all, but it does me, at least a bit. If I buy Nikon right now, I'm in effect saying it's fine that you stopped selling parts, made most of the independent shops stop working on Nikon, upped your repair prices, slowed your repair service, and lowered quality control. You were right to do so, because here's my money.
I say one part of me because there's another part that shrugs and says 'if it's the best equipment, it's the best equipment'. So myself and I had a long talk and reached a compromise. When Nikon clearly has the best equipment (D800e, for example) or best value (28mm f/1.8) then I'll buy Nikon. But when things are close and there is an alternative, I'll buy non-Nikon. The Tamron 24-70 f/2.8 VC and Rokinon 14mm lens choices made me feel better. I might also go with a Sigma 150mm f/2.8 OS macro instead of the 105 VR Micro. On the other hand, I really did prefer the Nikon 300 f/4 and 1.4x to the Sigma 50-500 OS zoom.
Buying Used Equipment
I don't hesitate to buy used equipment if the price is right. There's lots of used Canon gear out there, but often the prices aren't that great. Nikon and Pentax are a bit less available, but often at more attractive prices. However, the repair part plays into this too. If I get a great deal on a Nikon lens but then pay $500-$800 for a repair (typical cost for a 24-70 f/2.8 or 14-24mm f/2.8 rebuild) I've probably paid more than I would have for a new lens. The end result is I would be more likely to buy used Canon lenses and might save a few bucks. Like repairs, though, this wasn't a major part of my decision, but something I considered a bit.
I've already mentioned the 6D's Wi Fi hit my cooness button pretty hard. So does Nikon's gazzillion megapixels. So did the Pentax menus and the ability to map out hot or dead pixels from the comfort of my recliner. Of course, it would be even worse if I had the opportunity to buy a Pentax K5 II in one of the 100 horrible color combinations the Q cameras come in. What a great anti-theft device. OK, that might be just a bit too cool for me.
If the coolness thing affected me, it was in the 6D versus 5D Mk III decision, I think. I believe I overcame it elsewhere.
I mentioned earlier there were lenses I would buy to keep in my kit, but there were other lenses I'd 'rent' too, on occasion. Pentax falls a bit behind here for things like tilt-shifts, supertelephotos, and to some degree even wide-aperture primes (there are lots and lots of them, but many have slow AF, buzzy little motors, and other leftovers from older designs). You can get most things you want, but there isn't an all-you-can-shoot buffet like there the other two have.
I found this an interesting contrast from mirrorless systems where the I consider Pentax to have the strongest lens selection. It's the exact same set of Pentax lenses, which gives a nice perspective about the gap between mirrorless and SLR lens selection. Yeah, I'm probably still trying to make myself feel better for my all-or-none attitude when I started this.
There are a couple of lenses on the Canon side that I will definitely use a few times a year like the MP-E 65mm and the 17mm TS-E that just aren't available in Nikon or Pentax. I also use a 500m f/4 or 300mm f/2.8 a couple of times a year, but they're available for both Canon and Nikon. Ditto Zeiss lenses, which I do use fairly often. There is a 560mm f/5.6 available for Pentax but it's not available for occasional rental.
The Bottom Line
It should be pretty obvious that I decided against going with the Pentax system. It met all of my needs, there were things I really liked about it, but in the end the flexibility of the other two systems really attracted me. It was close, though, and if I had decided to just add an SLR with 400mm equivalent lens to a mirrorless system, I might well have gone with the K-5 IIs and 300 f/4.
Despite the better image quality of the Nikon system, I decided to go with the Canon. I waffled back and forth for days on this decision. In the end the biggest reasons were minor things that would not apply to many of you: availability of used equipment at lower risk, availability of a few specialty lenses that appeal to me, and a strong preference for the Canon 100mm Macro's IS system. I have to admit the 6D's built-in Wi Fi pushed my buttons, too. It's not just a toy, I really do use it quite a bit. I'm actually in pictures now instead of just taking them.
The system I got was not the best for image quality. Heck, I didn't even get the best Canon camera from an image quality standpoint. This did surprise me a bit because I spend all day looking at minute differences in image quality. I think I got the best system for me -- a hobbyist who likes to shoot some macro and hand-held telephoto.
If I shot differently, I would have made a different choice. You do shoot differently and will certainly make different choices.
Uwe Steinmueller, who runs the Digital Outback Photo blog has been kind enough to look at the same issue from a photographer's (rather than a gearhead) point of view and has written a nice counterpoint article. It's definitely worth a read (and the photographs certainly worth a look).
I'd love to say I'll not have any buyer's remorse, but I probably will. There are several D800 shooters working here that will show me images to make certain I do every chance they get. But overall I'm already happy with what I decided to get.
In retrospect, though, if I'd kept my Micro 4/3 system I probably would have bought the 6D, 400mm lens and 100mm macro, used both systems for a while, and then decided if I wanted to sell the Micro 4/3 system and add lenses. That would have been the more practical thing to do.
This long series is, at last, mercifully over. I appreciate the comments of those who enjoyed it and the patience of those who didn't. The simple reality is writing about it helped me organize my thoughts and my processes, and in this case I think helped me make a more informed decision.