I could mention that Omega was an amalgamation of many monsters through Time Compression, and that he was thus stronger, or that SeeDs are trained primarily to fight Sorceresses, buut...

Mostly, I'm just offering an alterative, internal explanation. Either is valid; it depends on perspective. From an out-of-game perspective, they're special battles put in for greater game challenge, yes. But, I like to be able to explain things without resorting to external things like that, as I like to occasionally roleplay or write fanfic in that setting, so internal consistency just makes that more fun.