The surprising thing is that Venusaur is so low on the 1337 stats. There for sure needs to be more love for Venusaur.
I also feel like the Manaphy usage is justified in some way. Keldeo is basically Manaphy to an extreme. Higher Special Attack and Speed make it extremely deadly to face, even with one Calm Mind under its belt it's way more potent that Manaphy. The thing is Manaphy likes to run bulky sets, which aren't very effective in this fast paced metagame with Scarf Genesect and all that.