I think the beta is pretty good.. i think levels like the cradle do good, but indoor levels like caves and facility call for smaller guns/characters for more spacial environment (i'm used to css).
However,, what I was really going to recommend;
combine levels like facility and runway together to make uber-sized maps..
You could also do connections like the depot and train,, and even crazier,, jungle and control... I suppose you'd be able to do it for dam/facility/runway,, as cradle is rather large too.. The aspect of being able to look from the first level of the dam to the runway to a certain degree (you can almost start to feel it around the tank area in the original n64 runway). Also making use of alot more doors and secret passages would be nice.
Multiplayer mods,,, such as capture the flag,, man with the golden gun, would be interesting to implement in options..
And as for my final stretch,, I think it would be a neat idea to add some multiplayer co-op scenarios like breaking people out of the bunker,,, or launching the moonraker space shuttle (was that really the objective in N64)? idk about GES, but CSS can hold up to 50 players, and you could have great objective maps out of the combinations of levels i was mentioning. IE: 4x40 (like in Perfect Dark where the weaker players respawn and try to kill the strong players).