Correction: AP Ammo does NOT deal 9999 damage each hit when you cast Meltdown - no! Not by far! Irvine deals ~4500 damage per Shot when using Quick Shot, and therefore he can only deal a maximum of 450.000 HP - that's less than Omega Weapon's half HP. When using Normal Shot, each shot takes about 3x times the amount of time, but deals, let's say 5000 damage. That's 500.000 HP gone. Some criticals (say you haven't got a high luck stat) can easily increase that up to 550.000 and beyond. So we've got a million. Assuming we get criticals often (example: 100 Ultima junctioned to Luck with Luck + 50%), we may just be able to defeat Omega Weapon.

So yes, Irvine can deal more damage in real time, but in "game-time", so each round, Zell can deal much more damage. And Irvine has a limit of doing so - unlike Zell.

Of course, you can take the liberty of maxing your Luck stat to 255 and make the critical hit chance 100%, (like the guy in the video i posted did), to get about 9000-9500 damage each Quick Shot. But I definitely won't spend weeks and weeks of bringing Siren to Lv 100, get 100 claws of curse (are they called this in english?), make them a dark matter and then a luck plus - no thanks.