IMO, the issue is right there. A good A+ Pokemon doesn't automatically make it a candidate for S rank.Mega Altaria is probably one of the best mons in A+.
I've used M-Altaria and although it is very good, it is a 'jack of all trades' Pokemon. The DD set typically runs adamant and thus is still outsped by 135+ speed and scarfed Pokemon at +1. The roost + 3 attacks is too slow. The bulky DD sub mono attacking set is harder to set up with and faces competition from regular gyarados, which is bulkier, has two attacks and good recovery with leftovers and bounce. Ive always found the bulky support set to be somewhat redudant to Sylveon and although M-Altaria can choose to go physically or specially defensive, I just feel that the opportunity cost for that mega slot is too fierce for M-Altaria to function as a cleric, especially since stall teams will reserve that slot for M-Sableye and probably be using Chansey anyway.
Personally, I've found the DD set to be the most effective and M-Altaria should stay as a solid A+ Pokemon. IMO, S rank is for metagame defining Pokemon that you must have at least 1 check for and M-Metagross, M-Sableye and Landorus-T fit that criteria well. I agree with M-Lopunny moving down since Greninja's ban has increased usage for bulky psychics and fairies and since I was on the fence on whether it should have been S rank before, this definitely makes it A+. The only candidates for S rank in my eyes are Clefable (which I don't think should rise but can see why it could) and maybe Keldeo. But M-Altaria needs to stay A+.