[Coda]

Neutral SHOULD be the all-around winner, and elements should be chosen based on a strategic advantage for the mission at hand. Situational advantages means that an item that would normally be a little bit behind the curve can really shine in the right circumstances. The problem is that Xover's leveling system makes "situationally useful" stuff far too much of a pain to achieve progression on, so even WHEN the elemental stuff would have an advantage, it's underleveled and therefore not likely to be worth it.

As for avoiding it always being about numbers: Combat-wise, one of the big points of divergence of the Mega Man X series from the classic Mega Man series is that elemental weaknesses in MMX don't necessarily deal more damage than, say, a fully-charged buster shot, but they have other effects in the fight -- interrupting attack patterns and taking control of the battle instead of just hitting harder.

Since I'm not familiar enough with the source material, I think it would be useful to see the first draft before making any more specific suggestions.