Okay I finally checked your alpha again, this time the last version Magnus posted. Here are my thoughts:
Let's start with a simple statement: your map is HUGE, I mean H-U-G-E, err... TOO HUGE! You MUST get rid of some routes and even complete rooms. You can play 8vs8 in this and not find an enemy while wandering around for a minute. Also the height levels differ too much. At the current state the slopes are way too steep so you will lose all your running speed resulting in a loss of flow. Bouncepad are nice, but they should not be the only option, since they make you a VERY (!!!) easy target for foes. Under normal circumstances you always (!) die while using jump pads and enemies chasing or fighting you. I suppose to get rid of the giant dual-grate-floor room holding the rail at the moment. Just make something smaller and more direct there. The key is flow, nothing is more important in a ctf map. If you got the flag you just want to run as fast as you can. So obstacles, complicated architecture, jump pads, traps, unclipped trim, etc. slows you down and annoy players. You must be able to strafe jump through your map quite easliy. The slower parts should be supply rooms with good items or complicated and dangerous short cuts. Remember, Q3 is a fast-paced action game

Also I found 3 RLs on one half of the map. Good indicator for it's size again. And as obsidian already stated, vertical gameplay only takes place in a few areas. The mid is a good start, as is the base. Frame those beginnings!
Next is the midfield, since it is the most advanced part at the moment. First of all it's design is pretty neat. I like the placements of the two YAs, the MH and the curvy, rocky look. Also the flow is good, so you can actually rush through the mid without making 32 trick jumps followed by 13 u-turns and other obstacles. IMO you should get rid of most of the lava/void. At the moment those pits are too large, so you'll drop into them by accident rather often (or will shoot into it with a single rocket, while having 200/200 or so). It's fine to have those traps, but they should be the minor part in the area where most battles are fought in ctf games today. Another thing is the route above the YA downhill into the own base. It's just too hard to defend. If an FC slips away along this path you have a small chance of killing him. This way is just too easy to go with too less time to spend in the dangerous midfield.
Now we come to the base. The size is okay, but the layout could be better. I fear it is quite indefendable at the current state. You've got round about 8 (EIGHT!) entrances to the inner base holding the flag. That's quite impossible to defend. Also because it just lacks armor, health, weapons, ammo (but I think the item placement isn't anything near final yet) and - more importantly - a place where you can defend the map without getting hit in the back. No camping spot (hell no!), but something where you are at least a bit safe and can lurk for enemies.
Also try not to use teleporters. They are somewhat deprecated in ctf. The one at YA is quite okay (dead ends holding item with a teleport exit actually work), the one behind the flag is unnecessary, also because it works both ways and doesn't bridge an enormous gap.
Another note to the YA teleport. Slow down the jump pad to it, so you actually have the choice of using the teleporter. IIRC at the moment this YA is only interesting for enemies invading your base or defenders running back, just because it teleports you back a long way into your base while wanting to leave it. Quite uncool.
Did you already think of PUs in your map? Nowadays ctf is mainly a fight for PUs since those defenders always got stronger over the years so you need the advantage of a PU to steal the flag. I did'nt come across a single one, but also played in ctf mode without sound, so I'm not sure. I'll suggets to put a '2 regen per base and 1 hast/quad (maybe alternating) in mid'-combo in (like p9 or p15). A double quad/haste could also work (like p1). Maybe you should place mh in base (respawn time 60secs), would strengthen the defence and putting a quad/haste in the old mh place in mid.
Another thing is the placement of the portable medkit. The placement is actually good (nice work with the stairs there, fits perfectly a31n), not are the lowering bars in front. If they stay down for good after activated, it's okay since they don't affect gameplay. But if they should act like a door, remove them as they will distract players.
Final encouragement (:D): The midfield promises good fights, the theme you want to create is great and I like the idea behind the flag room. I know, it's really hard to put together a good ctf map that will be played by the community (ok that's kinda impossible). There are so many good maps out there, that just don't get played because of really tiny flaws. I hope yours will be flawless!
I hope you don't feel offended by my post, it sounds kinda harsh, I must admit. But I see potential in the map and don't want it to get wasted. I hope I can contribute to this project as a regular q3ctf player with my knowledge and experience.
Greets maz0r (who hopes this didn't get too long and is quite understandable

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Edit: Fixed a stupid spelling mistake, so the sentence makes more sense now 