An experiece system like most RPG/MMO's
There's sooo many things you could improve on your caracter by lvl'ing up, and as long as it's FPS they'll still just be perks, and not WOW-style lvl80 beasts the living shit out of lvl 70 no matter what. seeing as how good you (the player, not the in-game character) shoots, and how well you play will still be the most determing factor.
You should keep your XP/bonuses from map to map like in an MMO, so you'll have the coolest part of the MMO's but in an FPS game, which is more action packed, and combat consists of more than "swicth between casting these 2 spells while the tank takes the hits" (yes i played WoW)
I know BF2142 has this to some degree, and even BF2 has weapon unlocks. But imagine if every badge in BF2 came with a little bonus, or some skill points so you could choose your own bonuses.
To give a few examples
New weapons (already done in BF series, but add as many weapons as possible)
New gadgets (cloaking device, jet/jump-pack, longjump, glider, mini-cams, hook/crossbow (like BF2SF) sentry guns, heat-vision (predator) etc..
Extra clips, larger clips, faster reload.
Increased run/walk speed, increased stamina(run-bar) faster stamina regen.
Increased health, faster health regen.
Higher weapon damage, faster rate of fire, more accurate weapons (smaller crosshair) specialize in groups of weapns like shotguns, SMG's, Pistols to gain these, or in every single weapon indivudually, or both
You could even add stats, to take care of some of the bonuses
Strenght: your crosshair moves less when spraying, more str lets you carry more armor and bigger guns without move speed penalty
Agiity: smaller crosshairs (precision), faster reload
Stamina: more hp and stamina, better regen for both.
Inteligence: dunno... perhaps as requirement for gadgets... or maybe gun-wielding psychos just don't need int.
Make a game that supports all sorts of modes from DM/TDM, old school CTF, BF-style CTF, VIP, multi-team clashes (more than 2 teams) make maps for small DM's like 8v8 and much bigger maps that support large scale combat like BF 32v32 or even bigger.
Make it support PVE maps as well, where players team up to take on missions like any co-op FPS
Take every good part from every FPS made, like the command-flower from BF2/2142 as well as mic-communication, get a good working clan-system.
For gods sake don't make it PC/console cross platform game. When you have to give the console aimbot, and extreme inaccuracy for the PC players it becomes screwed.
Chances are that most of the things i've listed already exsists in some games already, but these are just some quick thoughts.
EDIT: this is thought of purely with online multiplayer in mind
), which would have around the same number of players as M.A.G (256 players), and players will be split into squads of about 4-8. 
