next_ghost, great post. I agree with everything you said, but I have a different philosophy to your approach: I've long since believed the initial design weakness of tremulous was allowing more than one builder anyways. Just one commander in other mixed RTS/FPS games like "Savage: The Battle for Newerth" worked quite well, for all the problems you already outlined.
If I may, I say:
i. Only allow 1 designated builder each game (or x% amount of builders based on build points). Really, no more than say 2 for even those servers pushing the BP boundaries with 150 or more.
ii. At map start, in this priority make that designate assignment:
(a) Designate from the previous game is assigned that role again for this game.
(b) Query master or host server for regular player names (or GUID) against kick votes (or whatever other determinant) for that player.
(c) Randomly select from a pool of players on each team.
(d) or others.
iii. Immediately after a game starts, team vote can call a server side !allowbuild vote for any one player or the designate himself (even from spec) can !transfer designation to any other player (overriding the prior automatically assigned one).
iv. Most importantly, push spawning players off nodes/eggs automatically so others may spawn (or redesign the spawn interface entirely).
I already know what you're thinking too: what happens when those builders die. Who repairs? Who builds? Well, just reallow the ckit at the armory for all other players until the designate(s) respawn, or even newly spawned humans can grab a ckit if the designate(s) is dead, and a build expiration timer starts for all those other non designates. The same timer starts for non designate aliens who spawn as grangers too. Well, now you understand the importance of a builder (as it should be now with tremulous but isn't). You need to protect him. You need to help him. Shoot, if need be, beef up the blue ckit pringles can to a stasis gun, temporarily imobilizing aliens in base. Likewise, even give s1 grangers a trapper like spit as well. For either stasis addition (on aliens or hums), that defense weapon would only be effective in or around some buildable, like a turret or repeater or egg or whatever.
Otherwise, (like you say) you just have a bunch of players fighting eachother over build points or griefing servers into oblivion. And how many times have we asked in game, "Who's building? Who's repairing?" or "Why isn't anyone building? Why isn't anyone repairing?" Is multiple builders really what makes for fun game play anyways?