Interesting. With classes and flags, don’t we basically have a Fortress game? I’m not a Fortress expert so excuse me if that’s extremely ignorant.
It just seemed to me that that’s basically what defines Team Fortress: Flags and Classes.
Some thoughts:
I’d prefer the spawnpoints to be at special spawn areas (with team doors) but no spawntime. This way you’d have a lot less waiting time (more fun) and capturing a flag would be less lotto, because you can’t do anything against a full loaded player spawning right ahead of you with respawn protection. That’s not an issue in Q3A because you spawn without armor and weapons.
Do the items make sense in a class based game? I can see why ammo and medi paks would be useful, but the ammo makes the Field Ops even more pointless and the +5 health paks don’t seem very valuable, considering that Medics are the only really useful class on the map anyway (besides heavy weapons). 
I wonder if there would be any demand in a custom modification for this? I don’t have a really good idea for it though (just wasted several hours running around the map while trying to come up with any). The possible kind of modifications I could see working would be:
a) A real deathmatch modification, players don’t spawn with anything and weapons, etc are spread around the map as items. I can’t see this working very well with realistic weapons though. It would also be kinda sad to get rid of classes.
b) Changing the classes to better suit this kind of gameplay. Maybe making the game a little faster, adding things to construct and destroy for engineers, making medics real support classes, have classes that are better suited for offense or defense, etc. I don’t have many ideas how to do this with the WW2 theme of ET though.
c) Like b but with completely new weapons and classes, putting the game into some fantasy environment and making it more like a traditional deathmatch shooter with classes. Sounds like a fun project to me, but isn’t that exactly what the guys from ET Fortress are doing?
Maybe I should take another look at Q3 Fortress (goes searching his Q3 CD).