Thanks for the further input everyone. I'm glad everyone likes the trains so much.
I was aware of a bug with Valve's trains that you could stop them by übering a engineer who is pinned between one of his buildings and the train and the observed bug in my map seems identical to this sans über.
The map has three trains that it switches out based on the Blu team's progress. Strangely, the first train was impossible to stop via the method I observed in the demo (an über was required) and the last two were a piece of cake. Even more strange is that the trigger_hurts and func_brushes had identical properties (except names and parents). I turned on buddha and hurtme -1,000,000,000 and observed what happened at the point of impact. The first train tried to squeeze me out between itself and whatever I pinned myself against hurting me all the while. While the last two did neither of these things. Remembering back to a previous bug where I was able to stop the last two trains by riding them and edging off into the rough cliff face (a incredibly odd and undocumented bug) I deleted the offending entities and rebuilt them from scratch.
Anyway, some preliminary tests have found that that fixed the problem. I will post again after I get a larger sample. By the way, it's bad to copy named entities isn't it? (might explain why the red spawn doors were acting up)
I have already parented a nobuild to the top of the trians and it worked, but I like Political Gamer's suggestion because it would help counter-act stopping the train with übers and make it easier to build things adjacent to the tracks (won't have to worry that the train will snag it). As the trains are now you can only get a lvl 1 sentry up for 2 seconds before the train claims it, so I don't think track buildings are that great of a loss.
About the second point, I already plan on nerfing that little sentry nook. I'm thinking about adding a detail prop to force the engineer to build closer to the back wall. Also, I want to add some climbable props to open up the roof area to all classes (this would give people who want to flank the defense but don't want to run the gauntlet a second route). I'm also thinking about opening up the entrance near the blu spawn into the tunnel to all classes to enable the attacking close-range classes to slip past defending snipers in exchange for a more round about route.
As for the first point, I'm thinking the area around the point needs to be expanded in general. I was hoping the current point would be sentry, heavy, and pyro friendly, but it is clear to me now that unless the entire team goes one of those classes, those who favor longer-range combat would get slaughtered on the poorly armored battlements and leave the close-range classes to fight the entirety of the blu team en-masse. Blu needs less cover and a longer run to the point to whittle down their numbers and to disperse them a bit and red needs more room to maneuver and to retreat to. It is the first point so it should be relatively easier to cap, but I agree that it is far too easy currently. I was hoping that reinforcements would get a chance to retake the point by riding the train in, so my goal is to balance it to the point where red team can get one or two waves through on the train.
As for the frequency of the trains, I'm reluctant to decrease it too much because then the gauntlet becomes too easy to run, but I suppose it could be a bit easier. It pretty much forces you to run straight into the enemy, so some tolerance might help make it more viable.
As for the bi-directional nature of the trains... uh... well, I think it's justified for gameplay reasons (Well has bi-directional trains). The train provides blu an alternate route to C and prevents red from pushing back through the gauntlet as easily. I can understand the need for a better warning system for the switch. I plan on making some signs to place in the spawns to make it more clear how the trains behave and there are already some signals that change color when B is capped, but I could make those more noticeable. If you want a reason it's because when blu team captured B they became the majority stock holder in Radium Express Delivery (damn trust busting) and decreed that trains should immediately go the other way.
Again, thank you for all your input.