I wasn't around at the time, but the argument I have heard most often is the ill-informed one of redundancy. Of course, Chemical King's powers actually can be explained by science, whereas Element Lad's can not, so I've always preferred Condo's. However, CK's are typically harder to show without telling than EL's, so I understand the latter being better suited for a visual medium than the former, but this doesn't mean that Condo can't be done well.
Well, genders are just boundaries of normative behavior for each sex as socially constructed in different societies over the millennia. Humanity would be better off if we dropped the concept entirely and just let everybody be themself without any prejudices regarding how people like to dress or what they do with their own genitals and so on and so forth. But since we sadly aren't there (yet), I fully understand the desire to align with the normative gender of the other sex, even if using the same terms for genders and sexes makes things unfortunately imprecise for everyone. One would hope interstellar societies to have progressed beyond this by the time of the Legion of Super-Heroes, but that honestly feels to deep for Bendis - or the target audience - to explore, despite being a traditional sci-fi concept. That said, at least one Legion timeline so far has achieved literal sex changes (albeit through a rather improbable and ineffecient manner), so, if not on a philosophical level, at least on a practical level this should be able to get covered in this timeline as well.
Hear, hear!