I still play Counter-Strike (1.6) and they have a VIP game mode where the Counter-Terrorist team must escort one individual randomly selected on the team to a safe zone usually located on the opposite 'end' of the map. I realize that Natural Selection is built around the node system and that it's important to balance the weaponry/classes around that which is its core, but just think of this more as a 'down the line' idea. It could still use the node system, but add a few gameplay mechanics. This might not translate as well to NS2 though, since it isn't round based like CS.
Counter-Strike: Source, and GO have both not continued with this game mode, but I was hoping NS2 could pick up the torch and run with it. The VIP could maybe be 'activated' by the Commander after a certain amount of time (and within a certain duration), where one player spawns as a scientist in 'slow' heavy armour (for marines) or a 'hulking' disease carrier that treads along at a slow pace (for kharaa [you get the idea]). Once activated and spawned, the VIP would then need to get to the 'designated zone' (which could be static, or randomly spawned like the base placement at the beginning of a match) and the opposite team would try to delay them long enough for time to run out, or to kill the VIP. The VIP would also have a limited amount of attack capability with enhanced defenses (if it was being done in the same was as Counter-Strike's game mode).
VIPs could also be swapped out with objects that can be picked up by players, and passed along after death. These could be shown as 'artifacts' or 'ship hardware' to fit along with the games theme and not stand out like a flag (for example the Source mod NeoTokyo uses a robotic torso, to go along with the Ghost in the Shell and Cyber Punk feel of the game).
I just decided to ramble about this, and I don't really expect much to come from this post.
Thanks to anyone for reading though, I'll go back to playing NS2 now...