Why not make SMN's Bahamut do Megaflare when it's summoned

[Rongway]

I know this would favor min-maxing for more experienced players, but isn't it a valid choice for a summoner to have the option to choose their summons based on the situation?

There is choice and then there is "choice". Being able to "chose" between Bahamut and Phoenix would be "choice" because some people would choose the correct answer and some people would choose Phoenix.

All fights in the game are designed such that that healers can handle all the healing. Pulling out Phoenix to help would lose more dps than just letting the healers do the job themselves, so it wouldn't actually be helping at all.