I played KZ2 a lot online with our vgchartz clan, and I currently have logged 15 hours of my 2+ days playing time of MW2 online, not to mention all the time on MW1.
I have a 2+ K/D ratio in both of them.
Killzone 2 beats MW2 in aiming, I hate auto aim. It gives people skills they don't have, like hand eye coordination. I have got killed countless times because while tracking a person and aiming in front of them, the auto aim kicks in and jumps my crosshairs to their body and I squeeze my burst behind them and then they just tap their aim button and fire off some auto aimed rounds, I die.
Killzone 2 beats MW2 in graphics. The beauty of the multiplayer in KZ2 is awesome, especially particle effects. Firing into pillars in Radec Academy, while they slowly degrade as the the match progresses never ceases to amaze me. Lighting effects are awesome too.
MW2 beats KZ2 in weapons and class combination. I love KZ2 classes albeit it is kind of limited, but mw2 just has so many guns, perks, etc.. M16 plus stopping power, sleight of hand, last stand, my winning formula.
MW2 decimates KZ2 with its Killstreak reward. This is what separates them for me. My loadout Predator missile at 5 kills, Pavelow at 9, and AC130 at 11. I don't know what you use, but nothing is more satisfying then getting an AC130, and just wiping the floor in a ground war teamdeath match/domination.
Maps - MW2 over KZ2 I think KZ2's maps are more balanced and better laid out, but MW2 has a lot of maps included in the game, its around 15+, and lend themselves to a better online experience. You can pretty much be any class/combination in each map, play it how you want. And in real life, maps arent balanced, they are set up how a real environment would be.
Replayability- MW2 over KZ2. After I ranked up to the highest rank in KZ2 at 10,000xp(which happened within a week), their was no incentive to play again(they did add a 100,000xp incentive but that's it). I did however really enjoy playing in clan matches and earning valor with some of you. MW2 has so many unlockables online, now with titles, callsigns, barrack challenges, as well as prestige, their is no limit to how much you can play. 99.8% of people won't unlock everything. Whereas I unlocked everything within a week of playing KZ2.
Their are other categories I could go into, but let's just give the verdict. Each does things well, like KZ2's graphics and no auto aim, or MW2s killstreaks/classes. But it is the overall package, which propels one over the other. Without further ado the winner is....
Modern Warfare 2 is better than Killzone 2 online overall.
Fact: Earthbound is the greatest game ever made
