I've ran into these guys alot on the ladder the past days but I haven't really had much trouble dealing with them, perhaps because of the players I face or perhaps they aren't as good as they were last gen. Manaphy and Excadrill got obvious nerfs with the non permanent weather, making their abilities very situational.
Manaphy still has Tail Glow, which can do a number on defensive teams late-game, and Excadrill can eschew Sand Rush for Mold Breaker, which prevents Gengar from coming in for free.
Landorus, Tornadus-T and Thundurus are still really really good, the only change affecting them this generation is the weather nerf aswell, not letting them spam 100% accuracy hurricanes in rain.
Tornadus-T was the only one of these that got Hurricane. Landorus-I will probably be facing the boot soon since the set that broke it was the Sheer Force special attacker which isn't reliant on weather.
Genesect, Deoxys-D and Deoxys-S are pretty much the same they were in gen 5. Genesect still has the incredibly power U-turns with download boosts combined with a choice scarf or band. Deoxys-D is great as a hazard setter but can also be used for its super defenses. Deoxys-S is still probably the best suicide lead in the entire game with its blazing speed and access to spikes, stealth rock and taunt.
No arguments here, but Genesect did get Shift Gear, Blaze Kick, and ExtremeSpeed in between it being banned and XY being released, so if anything Genesect got BETTER.
I do feel that these pokemon might be slightly too powerful for OU but they certainly don't scream ubers anymore.