Thanks everyone for the posts. I am rethinking every aspect of it now.
That's OK. Making changes "on paper" is infinitely cheaper than making changes in the field. So
NOW is the time to second-guess EVERYTHING.
No help from the Electrical Engineer though. He is MIA.
In all candor, that's probably not a huge loss. An EE could be useful from a technical point of view on a large/complex project; but probably not so much for making value judgements with regard to usability, etc.
Latest idea is to go with 8' T8 fixtures.
I still strongly prefer twin-tube four-footers, in most cases. If you shop carefully, overall costs are comparable; and it gives you that much more flexibility in terms of placement, switching, etc.
How about this? Changed the two strips in the middle on separate switches.
Well, the overall layout seems to be something of an improvement over your original, in large part because you have pretty well obviated the overhead door blocking problem; but the switching still needs considerable work, IMCO.
In addition to the "all or nothing" problem mentioned by "nehog", your only control points for the main-area lighting are more than 50 feet apart, which will likely prove less than convenient in practice. There are any number of possible scenarios where you will want more and closer control locations. For example, suppose you're working in the wood shop, and are called into the house for some reason. Then suddenly you decide to STAY inside for awhile. You now have to trek all the way back to the woodshop in order to douse those lights, then again back into the house.
Or... You (or your wife) are returning from the grocery store, and pull into that middle bay. The garage door opener probably triggers SOME lighting (if only it's lame built-in bulb); but that's going to time out in short order. You/she open the trunk to find that several of the bags have spilled, and you now need to spend some time sorting it all out and putting everything back into the bags before schlepping it into the house. Would it not be preferable to have a switch/keypad RIGHT THERE that can be immediately used to turn on enough light to really see what you're doing? AND be able to douse it again as you pass through the threshold from the garage to the house, on the last bag-toting trip?
These are just two figments of my imagination, off the top of my head. I'm sure that there are many more possibilities, some of which will likely be impossible to predict until you've actually lived in the house for awhile. The point is, you want to maintain as much flexibility as possible in the initial design/installation, so that these "to be discovered" scenarios can be easily accommodated as they crop up.
Seriously, given all the possible permutations which COULD come into play in a shop/garage this large and this complex, I want to beat the drum again for using Insteon controls. I have no doubt that, particularly in this case, it could significantly simplify the switching arrangements; and it might actually turn out to be LESS expensive to install as compared to implementing enough "conventional" switching to have as much flexibility as you'd ideally want. And trust me, once it is installed and set up, it would be MUCH simpler/easier to live with on a day-to-day basis: No more having to throw a half-dozen or more switches to turn on (or off) all the lights you might want to run at any given moment; and more importantly, no more
remembering which half-dozen switches you need to throw!

:
As for installation simplicity, consider: Running one 14/2 cable to a single-gang box wherever you want to have control will allow you to put in one of those six-button keypads at that location. And that keypad can be set up to control ANYTHING (actually, EIGHT "anythings", in any combination, presuming you add the 8-button change kit
http://www.smarthome.com/2401WH8/8-Button-Change-Kit-for-KeypadLinc-White/p.aspx). Compare that to a whole row of conventional switches AND the convoluted wiring running all over the place needed to implement traditional 3-way or 4-way switching. Optionally, at the main (i.e., most commonly used) entry points, make it a two-gang box, to support two such keypads; but notably, that same single run of 14/2 will still suffice. Simple, cheap, and effective. At least most of the loads themselves would actually run off those in-line control boxes I previously cited; but if you want, a few fixtures (such as perhaps your "walk through" lights) could be directly powered from the Keypads and/or Decora-style SwitchLincs. And because most of this would effectively be simple "in-line" wiring, installation would be significantly simpler and you would likely use LESS materials overall.
Part of the point here is, the vast majority of Insteon products are designed to be retrofitted into conventionally-wired homes, and will work just fine in such applications; but if you KNOW going in that you're going to use Insteon, you can greatly simplify that underlying wiring, gaining both usability AND cost-effectiveness in the process. Please don't dismiss this idea until you've put some really serious thought into it. I think if you do put sufficient thought into it, you'll "see the light", so to speak.
A few other semi-random thoughts...
I suspect that you still have too much general area lighting in that upper-left bump-out, at least presuming that you really do have GOOD task/under-cabinet lighting in there. But as long as you break up the switching so that you don't HAVE TO turn it all on at once, it's probably not a disaster.
"All or nothing" switching is probably OK in the wood shop; but even here, it wouldn't hurt to break it up into two banks, MAYBE running off two different breakers. I'm thinking specifically of the scenario where one breaker has tripped or is shut down for maintenance; in which case "all or nothing" leaves you with "nothing". I'm less certain about the AMOUNT of general overhead lighting you're showing; this will depend greatly on the task lighting you wind up with.
I note that you have added ceiling fans in two of the garage bays. Why not the third? And either way, what about switching/control for these devices?
You're showing two banks of exterior lighting. I suspect that the ones over the garage doors are primarily decorative, and the others are probably floods of some sort. Presuming that guess is correct, I think I'd want more such flood lighting than you are currently showing -- at least one dual-bulb fixture at each "corner" (be that an "inside" or "outside" corner) of the exterior walls. Ditto for each corner of the house itself.
And again, the switching/control for these lights is sorely lacking. For the over-the-door lights, you're showing only one switch location, and in a rather inconvenient spot, at that. Do you REALLY want to have to walk out there to turn them on and off each day? As for the security/flood lights, you aren't showing the switching/control arrangements at all. I would want ALL of the floods controllable by one-press "panic buttons" located at SEVERAL locations throughout the house and garage, in addition to some form of automated control (probably based on motion sensing; but you could also tie it into a real security system, if such will exist). Need I mention that this is an ideal application for Insteon?
Obviously, this whole sub-topic needs some work. And note, particularly for the "decorative" exterior lighting, some degree of routine automation (be that timer-based, or dusk/dawn, or some combination of the two) is almost de rigeur. Again, Insteon will help here.
If I understand your sketch correctly, you're now showing additional outlets in the wood shop area and the third garage bay. That's fine, as far as it goes (even if every four feet is well into "overkill" territory; I'd probably go with a two-gang box every 8-10 feet or so); but outlets in the other two garage bays are now rather conspicuously missing. While I would not suggest that you need as many outlets in those areas (which are presumably intended mostly for routine car-parking) as in the "working" bay, those bays probably ought to be served by SOME outlets, just to cover contingencies (say, plugging in a vacuum cleaner, or a portable battery charger, or...?).
Finally, while it might appear that I am "nit picking", please don't take my comments the wrong way. I'm deliberately "playing Devil's Advocate" here, in an effort to ensure that nothing gets overlooked, and that your plans get as refined as possible before being carved in granite. You ARE "getting there", so to speak. So chin up, and press on...