As far as rail capacity being too much to keep track of ... no, not at all. The idea is borrowed from the old hex-based wargames put out by companies like Avalon Hill, and if it's so popular in a boardgame format to be included in nearly all those sorts of games, I can't see that it would be too much to manage in a computer game. You'd start your round, see in the box where gold etc is displayed that you have X rail points left, so it wouldn't be at all difficult to keep track of.
However I've been thinking lately of an MM problem related to capacity models, and that's that it still won't prevent people from trying to move massive armies about. Sure, good planning will mean that you distribute your forces in sectors so that ideally, if a war breaks out along one sector, the forces will already be there and your capacity would be enough to move all your new production in to replenish. But, that's ideally. If things start going bad in that sector and your flow of new production isn't enough, you're probably going to want to try to redeploy extra units from other sectors. Or, if a sector collapses, you're going to have to conduct some massive relocations of forces to cope. Though accurate, this will result in the same problem as limited rail movement, that is, too many units moving at a crawl and alot of tediousness.
So ... I'm now thinking about an even more comprehensive system that will really reduce MM while allowing for a higher degree of accuracy. A general movement allowance for all units in all eras, by road or by rail or otherwise, abstracting a whole bunch of factors like logistic capability, infrastructure capacity, command and communication limitations, unit fatigue and other things. You'd start with some base movement allowance, which would be modified by things like the military trait, certain key advances (in the early age things like writing and horseback riding for messengers to help with command and control, later on things like the steam engine, telegraphs, and eventually diesel engines, computers, satellites, and realtime C&C capabilities), and perhaps some Wonders as well. Also, Mobilization would be a huge modifier, perhaps doubling your move allowance or something. Moving a military unit would take up a point, and that's all you could move in a round (nonmilitary units like workers and settlers being exempt, though).
Now that would add some real strategic decision-making as to how to maneuver your forces, and because of the limitations involved, MM would be vastly reduced. Instead of mindlessly cycling through 100's of units every round, you'd look over your empire, decide where you needed more units, decide where to draw them from, and move your limited number.
Other possible benefits of such a system: faster turns (good for multiplay, also allows increased turns between tech advances so there could be a WW2 in the span of only two or three advances), no galleys sailing around the world and returning to find an industrial society by the time they get back, giving a chance at a military role for smaller civilizations, and a better representation of the role of logistics and command capabilities in warfare of all eras.