It still has the highest neutral DPS in the game after Deoxys-A which makes it the fastest practical generalist. MM won favor for being more bulky and having more resistances which adds to its bulk. Against Palkia it will be a go-to counter even against Draco Meteor since it's DPS is so much higher than anything else.
The effectiveness rebalance hurt its foothold as being the top counter to itself. Jynx, IB Mewtwo, Piloswine, and Weavile all enjoy higher DPS than it now while lacking a weakness to Outrage. Mamoswine, Glaceon, and Regigigas do too but they're unreleased right now.
I have a maxed Rayquaza I've used in PvP. Giratina's spammy attacks have spoiled me since Rayquaza takes noticeably longer to use Outrage but if unresisted it obliterates damn near anything.
All in all I think it's lost some footing since many dragons are doubly weak to ice, but it's still a beast. Am looking forward to its return, whenever that may be.