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I'm gonna get flamed hard on this one I'm sure, but if you break it down MW3 pretty much outdoes most standard MMO's out there regarding PVP, even if you use the typical definition of what makes a game an MMO.
1) It has a leveling system almost on par with any standard themepark. In fact, it goes to 80 LOL. At each level you unlock either a new weapon, a perk (e.g., trait or skill), or a kill/death streak (e.g., special attack). In fact, it allows you to "prestige" and start the level process over again, with a few minor twists thrown in. In fact, each weapon you unlock levels up independently as well. And there are regular and "pro" versions of skills as well.
2) All the PVP is instanced, true, but seriously pretty much every MMO out now is 90+% instanced. And the instances are simply better and more diverse in MW3. Considering: 18 completley different maps in MW3 (at launch, more will be release in expansions at least 2 this year), with each of the 18 maps supporting literally dozens of different gametypes (deathmatch, search and destroy, capture flag, domination, infected, etc with hardcore modes, normal modes, etc.). Plain and simple, the variety is much much better than any other instance MMO
3) The way people build their characters plays different, just like an MMO. You've got your sniper, your run and gunner, your camper, your shotgunner, silent types, fast types, etc.
4) Waiting for a new match takes only seconds, at any hour of the day. There are millions queued up at any given time for a match.
5) Statistics and rankings are superior to those found in an MMO. You can track your rank in any number of statictical categories amongst millions of others. Based by gametype, gun, etc. Better statistics than any MMO.
6) There are clans that compete competetively, just like an MMO
7) In fact there is even a story. A campaign that you can work through. It doesn't impact PVP just like GW2's wont either, but it is there.
8) It is purely skill based. Not tab target. Environment plays a huge factor. Some materials block bullets entirely, some only slow them down. Bullets dont track you behind a tree for instance. If you are good, you will crush. If you suck, you will rage quit. No hand holding.
So, I know I'm not breaking any new ground here on these points, but I just think it is sad and pathetic that an FPS, even a supposedly shallow one like MW3, pretty much blows most other PVP MMO's out of the water even when judged as an MMO. Very sad.
But, the silver lining and glimmer of hope (for me at least), is the rumors of a AAA FPS MMO being developed by Bungie/ATVI/Blizz. To be honest, the FPS developers are just plain better than the MMO developers. The FPS developers will provide the innovation the traditional MMO developers have been incapable of, at least regarding PVP...
GW2 "built from the ground up with microtransactions in mind"
1) Cash->Gems->Gold->Influence->WvWvWBoosts = PAY2WIN
2) Mystic Chests = Crass in-game cash shop advertisements