Alright, my idea is large outdoor maps, but not necessarily spacious, ie urban areas, mountain range, a large field with a complex system of caves directly below.
Now, to the marines. Keep basic marine armour/weapons the same (add some new of each), the major addition would be squads and vehicles. 1 General, an overall commander who plans the full field of the battle, assign base building waypoints and what kind of base he wants (read: not individual buildings). He does, however, have complete control of the home base/drop point and its defenses. 2 or 3 sub commanders, map-dependant. These handle the orders given by the general, as well as squad commands and individual construction.
Squads: Consist of 5 marines, plus a sergeant. The squad works as a team. The sergeant is the only one with communication with the rest of the command net, the other marines can only hear/see what their squadmates say/type. If the sergeant dies, a warning is sent out to the commander in charge of them, he then assigns the remainder of the squad to assist/reinforce another one over an emergency channel.
Vehicles: 3 classes, heavy assualt, light assualt/transportation, and air.
Heavy:
Tank, 1 main gun, two front-corner mounted machine guns (operators exposed), 3 or 4 marines can ride on the side a la halo.
Howitzer tank, 1 main gun (launches high cal mortars), 1 mg front mounted, 2 possible riders
APC, 1 mg with operator inside, 1 rear mg with operator slightly exposed, can carry one squad excluding driver (mg opers included)
Drill tank (underground only) can drill new tunnels, has a main gun mounted in front and a rear mg (this requires destructable terrain, like red faction)
Light:
Assualt Jeep: warthog ripoff, rear mounted mg, one side rider, one driver, 1 marine can also ride in back with mg.
Transport truck: 1 driver, 1 passenger, 6 marines in back (can look over sides to shoot)
Bike: 1 person vehicle, no weapons, extremly fast, used by commanders/scouts
Attack ATV: 1 person motorcycle, front mounted dual machine guns, slightly slower than the bike.
Air:
Dropship: holds 6 marines, two of which operate mg turrets placed on either side of the fuselage. 1 pilot, with forward facing, low powered heat seekers, mostly just for harrasment. (very effictive against alien heat signatures) Not very maneouverable. Marines disembark by landing or jumping, after parachutes are researched. They cannot fire while jumping.
Helicopter: higher powered heat seekres, forward facing mg, 2 marines in back, manning a side firing mg, a la vietnam choppers. (2nd marine is busy with ammo belts)
Jet fighter/bomber: forward firing mg/missles, bomb bays capable of holding 10 dead reckoning bombs, can be upgraded to gps targeted (targets set by general)
Now, this may seem to be way overpowering the rines, but heres the alien stuff.
4 types of body frames, small, medium, large and giant. small being skullk sized, medium fade, large current onos, giant, alien version of a biological tank, literally the size of a bus. These types give inherent hp/ap values, as well as speed modifiers.
Major evolutions:
Wings (only on small to large sizes)
Gas flight (zepplin style, on large-giant only).
3 levels of armour, light, medium and heavy. Heavy cannot be used with any kind of flight. All give speed restrictions.
Legs: bipedal (required for wings, less weight availiable (each upgrades adds/subtracts from total weight)), quardruped (higher speed, more weight avaliable), centipedal, required for giant lifeforms, can support most weight, is slowest.
Arms: none (required for wings), One (required for builders, can lift the most weight), two and four.
Digits: claws, builder extension, manipulators (must have two arms, allows the alien to operate basic marine epuipment, such as less-complicated weapons and welders), blades (fade style)
Other weapons: here goes bile bomb, acid rocket, etc. Note that all lifeforms have the basic bite attack, although size and number of arms, strength, etc affect damage.
Note that for giant lifeforms, they have the option of a hollow body, which will allow them to carry other aliens at the cost of health. for flyers with hollow bodies, they can carry a supply of acid packets, provided by a builder, to drop as bombs.
Attributes:
Armour: Decided by weight and body type and related upgrades
Health: Decided by body type and related upgrades
Strength: Decided by body type, number of arms/legs and related upgrades.
Basic attacks: dedided by number of arms, legs, etc (four arms will have a swipe/claw/punch attack instead of bite.
Intelligence: the more of this an alien has, the higher level marine equipment it can use. Determined by body type, digits, arms, legs, and weight. Those values closest to human will give higher intelligence. Also, evolving certain upgrades, such as cranium capacity, symbiote will increase it, while adrenaline, strenght and such will decrease it. Note that an alien MUST have manipulator digits to operate marine stuff. If extremly close to marines physically (ie bipedal, two arms, medium body size, similar weight, stregth, etc), can wear the marine body armour. This brings up covert infiltration, especially while in heavy armour.
Gameplay modes: two major modes, both having submodes that are the actual different types of games, like co, ns, war, etc.
Campaign: Character is built upon and saved, similar to a battle.net system. Alien evolutions, marine armour and tech, weapons, personal vehicles, etc are all saved. The character is given a power rating based on it upgrades, similar to wh40k. Team fairness is determined by these values. You can upgrade you character in game to whatever you want, it will not be saved, but through the menus you can use stat points to buy base upgrades that you will always spawn with. This is undoable. You gain stat points by playing well, winning games etc. Before you cry imbalance, refer back to the advancement points idea. Now, this invites hacking the char files, so have all files on a file server. all files are read-only, and the server modifies them based on stats reported by whatever server the client is playing on.
Skirmish: classic style, everyone starts equal and builds up in game.
Now that ive spent my hour typing this, im sure many will have many problems with this, but keep in mind this is very rough, everything is suspect to change, and it all assumes that ns2 will have a very capable engine as well as at least 64 players erver caps.
I have purposly left out buildings because im out of ideas for now, and tired of typing

On a side note, i wouldnt mind seeing the current version of ns ported to the ut2k4 engine and have a few stuff added, not that itll ever happen. That engine is certainly capable of large maps and all sorts of vehicles.