Thanks for the feedback guys. I went ahead and burned through a3 and a4 by puggin the map a bit. Its a ton of fun in 6v6 (seems that way, at least).
I've made some changes for A5. First, theres an additional building in the middle area, at the edge of where the medium health pack used to be. You can get up their by rjing, or by leaping from rock to rock as a scout. I've also extended the platforms for snipers, as well as making the tilted roof near them acessible.
Next, I adjusted health packs around the map. The medium health and (now) medium ammo at mid are now located in the new structure (you have to duck inside to grab health). I've added two small ammos to the middle cap area, as well as a medium near each teams base (at the bottom of the ledge) and another small near the end of the cargo containers. Not sure if this is too much ammo, I'm really worried about sentry farms. Hopefully the sight lines will be enough to ensure that any sentry gun can be taken out relatively quickly. I also changed the position of the small health and ammo below the spawn doors, putting them into the intel room. This should help alleviate some of the spam that will be coming from above, and give any attacker nabbing a flag a minor ammo pick up.
Next, I put the defensive ramps to the pipe bridge inside the intel room. This should make the intel room itself a more likely position for the defenders, and ensures that they have to walk by the intel at least once to get to the top (so they know where it is, and they can stop anyone they happen to see). I've also lowered the upper part of the middle building by a bit, making it much more rocket jump friendly and a more likely place for combat.
Finally, I went through the map and put a variety of interesting scout perches. The rocks in middle are now double jump accessible, let you get to the roof of the new building, and you can even circumvent the entire main combat arenas if your careful with your jumps. Likewise, the intel rooms have computer bays, allowing you to leap to the top of a lamp and then to the pipes or the railing. It takes a lot of skill to pull that off, so I'm hoping it won't be too abusable.