If my opinion counts for anything, I would strongly support option A (all Pokemon referred to as "it") - mainly because that's my instinct and what I feel comfortable writing (it's annoying to catch yourself and suddenly realise you have to go through everything you've written giving the Pokemon a gender), but also because I would agree that he/she does not sound right, Pokemon as objects is the ingame precedent, and the "Pokemon that are obviously female" thing is simply too vague, as it entirely comes down to personal opinion, which isn't the best way to form a lasting rule.
In regard to the who/which thing, I really don't care that much, it really comes down to whether we want to be consistent and, of course, whether it really matters. It doesn't have that much to do with what I outlined in the OP, but I would be quite comfortable with any ruling