I'm not saying that we should go by Nintendo's Species Clause. If it were up to me, we wouldn't! The point is that if we use "Species Clause" as Nintendo has made it, then we cannot allow two Pokemon of the same species on the same team, regardless of form.
However, this does mean that different forms of a Pokemon are treated as the same under Species Clause. Considering that we treat the different forms as different Pokemon for competitive purposes, Species Clause seems to clash with our beliefs in this respect.
I believe we should at the very least create another clause that would allow the unique forms to be used on the same team--except for the alternate Rotom forms; I don't think they're different enough for two of them to be used on one team. Why should we always disallow them? As far as I'm concerned, different stats / different typing = different Pokemon.
Should we use such a clause in ladder battles, though? I'm not actually sure. I don't see enough of a reason why we should, but I don't see a reason why we shouldn't, either. I don't think we would NEED this clause, but Species Clause seems lacking with respect to different forms. I need to think on it more. I'm definitely open to others' opinions on that.