First things first, shrink the last two points. They are WAAAAAY too big, both horizontally and vertically. The buildings are very tall, making the players feel small and making the buildings feel empty. Graza wrote a great guide on scale in TF2, I would HIGHLY suggest you read it carefully, then redo the last two points to more accurately fit recommended lengths and distances.
http://forums.tf2maps.net/showthread.php?t=12605
Now, specifics. Let's start with the second point. It's way too big, there's no good sentry spots. The first impulse is to build in the corner near the cp (can be seen in the second of your screenshots), but attackers coming from the opposite side can easily out-range it. If you set up on the opposite wall or on the balcony, then attackers coming in from the raised platform can out-range it. This frustrates engineers, and forces a team to have multiple engineers to defend a single point. Shortening the room by moving the wall opposite the upper entrance closer to the point could help with this issue. Also, when you do place health and ammo (really, there's no reason not to do this. It takes five minutes.) make sure you place them in areas where you want to encourage engineers to build - because they will likely build around them.
The last point is worse. First, it has the same issue as the second point - any sentry position can be out-ranged, and the sentries that cover the doors can't cover the point (and vice-versa). Moving the respawns and the control point platform much closer to the building will help with this, or blocking off the middle and forcing attackers to wrap around the sides. Also, shrink it a bit horizontally - attackers taking the far flank can easily out-range sentries. Adding some cover will help with this problem, but it is NOT a sure-fire way to fix. Throwing in tons of cover will just make your map feel cluttered and bloated.
Furthermore, attackers have WAY too many entrances into the final point. Two main doors on the ground level, one smaller flanking door on the ground, two in the upper deck, and one far flanking path. SIX! SIX paths that blu can take. Not only is that far too many to defend, but it splinters the teams up. You want to keep teams together and focused, to promote teamwork. Usually, attackers have one main route and two side routes (usually one which flanks around the main route, and another that flanks farther in), or two equally used routes. Cutting off two, or heck, even one of the bottom doors (get rid of the smaller one) would help this, along with removing one of the upper paths. The far flank is okay.
I would comment on the middle point and the paths between the points, but unfortunately almost all combat happened in the first/last two points.
Also, this is why you always have alltalk on during early tests like this: the game updated, rendering recorded demos useless.