I wasn't able to play the full version of the game but from what I have played involved mostly round 1 and the first half of round 2. I have to say that there were layout issues that hinder the game play (if you intend to have this taken seriously), and some small things that I found that bothered me while exploring the map. I'm not an expert in map making, so you disregard my advice.
Blue Spawn R1
Now, most of the changes here coincide with changes of the layout of CP1.
Pic 1:
Note 1: Increase size of drop floor to allow for up to 16 spawn points for this first spawn. Add Stairs for the left exit (the only one without stairs) and (following my proceeding advice) remove the door at the top of these stairs. If you decide to change heights in the spawn, remove the stairs all together.
Pic 2:
Note 2: I do not like this hallway at all. Its the fact that the spawn it so close. During game testing, a demo had launched pipes down into the spawn when the door was open. My proceeding advice about the layout change would be better suited.
Pic 3:
Note 3: Now, this is the majority of Blu's flow from their starting gate towards the control point. Now, the red "X", represents the stairs. I found the stairs to be troublesome for the Blu team only because it gave red access to get behind blue. Remove the stairs all together. Blue doesn't need access up here if they can get up there from their spawn. Usually the defenders for the first point don't need as much of an advantage near the starting gates.
The yellow area represents your unused area for the starting gates. I feel the movement of one of the starting gates from Blu Spawn in this area would help out the attacking team. A door that could be removed is possibly one near the "battlements" or the door below it. Personally, during the round played, a blu player can get corned in this area without escape.
Pic 4:
Note 4: Here's the fore-mentioned layout changes that probably could be implemented. Note that the door to the "battlements" has been move. Again, remove those stairs, and possibly add another path to the right of spawn as indicated. You will probably have to look over the heights to see how this may work but this is my final suggestion for just the spawn.
Capture Point 1 - R1
The following suggestions also coincide with Blu's spawn suggestions. The vast problem I have with this layout is a few paths that are feeling unnecessary. Also, playing this, for the first time, not seeing any of the previous version before, I found the layout confusing and tight. Let's begin!
Pic 5:
Note 5: This path, as I heard was recently added, fell under annoying to climb. Being forced to jump up here made the path feel less helpful than needed. Remove the lumber piled and add a ramp up to the new path.
Pic 6:
Note 6: In this particular area, I'd like to address a few issues I didn't like about this room. I felt that the capture point and the surrounding area was too cluttered and had feasible size deducted from it for paths leading up to it. Props in this area like the rockets and the records inhibit some of the game play for areas around the point.
First, the upper path that only Blu seems to have the most access IS a little too tall. Playing on this area, I fell to my death playing as medic, while trying to heal comrades. The drop off the upper area is high enough that everyone takes fall damage. The lower path, with the full health kit should be nuked. In my opinion, these two paths would opt better with having shared ground. That would entail also having the path be widen for game play as well.
Pic 7:
Note 7: There are addition paths here that need to be nuked. First, the far right from blu spawn to cp 1 has this wall hugging path that climbs the wall, heading to the vent. This feels too ambitious and allows for the attacking team to control the highest point over two areas. Nuke both the path and the vent up here. It is not needed.
Also, the blu in this picture is a quick feeling that the displacement of these two areas should meet rather than forcing a tight path up the stairs.
I'm having a hard time suggesting other solutions to the layout of CP1. My concerns are how complicated the layout feels with the multiple paths that cross over so much. Reduce the paths a little to help flow, increase and decrease as you see it. Hopefully you'll find a more definite solution by the following alpha release.
Notes and Final Concerns
Pic 8:
Note 8: Small note about this particular ledge and how it was hard to get over it without jumping. Clip it or some other solution.
Pic 9:
Note 9: Wasn't able to play cp 2 as much as cp 1, but here is one area I feel could be better done. The "battlements" of cp 2, the room with the generator, could instead be located to this window area. If you had continued my advice about capture point 1, the "new path" that was mentioned in pic 5, would instead be the area where the team could vitalize more. Change out the window area for at least one door, walling off access area, and if you feel you really need it, you could add windows still. The upper area, with the red "X" would change with my suggestions, but in use of area #2, would be cut completely.
Note that I've also included a stand of some sorts for the window drop. And a block that would cut down sniper lines a tad.
Finally, there are more issues to address that I haven't been able to get to. I noticed that Red's spawn with the train could use a vast improvement as well, but that will have to come at a different time since I wasn't able to be there to see it in action.
Secondly, I am concerned about optimization of this map. I've noticed right off the bat that most of the map between capture point 2 of round 1 and capture point 1 of Round 3 share a lot of open area. My concern is about frame rates and such. Round 1 and 2 could easily be cut off from each other that its not really need to show the former area. You may want to consider in map redesign, how to block up areas into pieces better for frame rates and such. I wasn't able to see how you've gone about doing this, but it was a strong concern of mine.
Man, hope someone takes the time to nit pick my own map like this.