It's simply too late to be considered S-Rank. They dominate very late game, yeah, and that's why they are A, but they aren't the best of the best because they aren't a part of enough fights...But for Kyogre, you still have to fight the 8th gym. The rain makes you battle quite a lot of annoying Swift Swim Pokes, including Swift Swim Horn Drill Seaking, Swift Swim Lovely Kiss Luvdisc, and Swift Swim Ludicolo. Not that they are horribly difficult but Groudon makes it a lot easier than Kyogre.
After that, Groudon plows through the E4, especially Glacia and Steven. Glacia's team wastes turn using Hail and is destroyed by Eruption. For Steven, 5 of 6 Pokes of his are weak to Groudon's STABs AND his trump card, MegaGross can do zero to Groudon.
Groudon makes everything after its capture very easy, a lot easier than Kyogre's. I think it deserves S-rank.