TAB KEY>
Tab key: Interesting, I don't use tab all that much when programming, I guess auto indent/auto format works pretty well (I code Java and a proprietary script language using Eclipse). As for program switching: I assume you use pinky (Command) + index (Tab)? I use thumb (Command) + pinky (tab), wouldn't say one way is better than the other. I thought about putting Tab to the thumb area, but that would be uncomfortable for one-hand program switching unless I'd put Command somewhere else, which I won't do.
Bracket keys: Don't have any problems with bracket location any more, though they took some getting used to, as I'm sure they did on the TE as well. They're not much further away from the home row than on the TE either, you have to skip over one row to get there, and less pinky spread is needed. Switching tabs in a browser I usually do by tilting the mouse wheel left or right (I'm quite particular with mice as well, they must have at least 2 thumb buttons as well as a tilt wheel)
Curved circuit board feels less solid: Aye, compared to the flat and heavy TE it does feel less solid. Luckily this isn't an issue when typing.
Firmware/compatibility: Been using Kinesis with OS X for 4 years without issues. Dunno about any CapsLock beep, but I don't have CapsLock anyway. Most if not all sounds are configurable though. I love the Kinesis's remapping ability right on the keyboard, though if TE ever release remapping software it will most likely be more more adaptable. Not hot on in keyboard macros, I don't use them on the Kinesis either; I do however use a software that does text replacement system wide (Typinator). Programing firmware oneself is very intriguing though, because of the ability to add extra layers with fn keys.
Price: TE is cheaper, and it should be given it's easier to produce (flat vs curved). However I see no reason to compare it to the Advantage Pro, which mostly adds more macros and a footswitch.
Switches: They added a red switch option to the Advantage some time last year, I'm typing this on reds (upgraded board which had browns originally).
No clue how well blues would work on the Advantage, but I'm not usually a clicky fan. I thought I liked tactile, but interestingly I prefer reds over browns on the Advantage.
Blank key caps: Aye they're not available from Kinesis any more, which is a shame. I hope the replacements I ordered from WASD will be nice.
Options (physical layout): no need to count key caps twice, so the TE has 3 options: 104, 105 and 109. The Advantage has no (physical layout) options in my book.
Hand separation: Pros and cons for either I guess... I haven't use TE too much, but it didn't feel less comfortable for the short periods I used it.
Pedal/cover/wrist rest/crud/USB hub: Shrug.
Center area: Would love some extra buttons there, as I said in previous post at the
functions keys bullet. Have to agree that the smaller width helps with mouse position.
Double shift caps lock: Hmm, I wouldn't mind a double shift caps lock feature on the Advantage from time to time, since I have no Caps Lock key, but no such luck on mine (4ish years old).
Thanks for the extensive list of things you like. It hasn't changed my opinion, but was interesting. The issues you have with the Kinesis I don't have or don't agree with, and some of the stuff I do agree with are comparatively minor for me (F# keys, wasted space). At the end of the day I think I love the Advantage's thumb keys way too much.