Aliens have a major advantage in the game regardless. If the aliens can get stage 3, they will almost always be able to even the game out. On the other hand, if it's s2 humans vs. s3 aliens, they don't (and never will) have a chance. Allowing armouries to be rebuilt would make the human SD more even to alien SD, but I think it takes away any likelihood of a lucky alien win.
So I have some ideas for sudden death that would make things interesting to say the least.
My first idea was to make sudden death more sudden and to really give anyone (even a rifleman with no armor) the chance to end the game. And that is simply that once sudden death rolls around, all defensive structures (turrets, teslas, acid tubes, trappers) stop working. Spawns cannot be rebuilt.
This would mean that a team trapped in its base will always lose when sudden death comes around. But if anyone can escape, they can end the game (if dretches can attack buildings).
As a side effect, I think that it encourages hiding. So when the timelimit comes around, and if there is a team that cannot respawn (but the other team can), the team the can respawn wins. Otherwise it is a tie. (A lone armorless rifleman could tie the game, but not get the humans a win if they can't kill off the aliens.)
My second idea was fairly simple: limit the number of respawns allowed during sudden death (default 3?). Don't mess with the build points or anything like that. That way, I think that a human team that is doing well during the beginning of the game can't lose in 20 seconds when a couple tyrants maul their base. But at the same time, it encourages spawn camping during sudden death, makes SD less fun for newbies, and makes it even harder to get to the next stage. (To prevent people from reconnecting to get 3 more respawns, don't allow spectators to join during SD.)
I don't know if either of these would work at all. I just think they might be interesting. (And they make "sudden death" more like its name.)