1º) Pal, Mewtwo creating that storm was merely a potent version of him using the move "Rain Dance". He was using that move, even before it was revealed in Johto, just like he later used the move "Shadow Ball" against Mew. Zekrom did something similar when he appeared in front of Ash in the first episode of XY, as he created an electrical storm. Dialga, Palkia, Giratina and Arceus can do much more than controlling the weather, the can warp reality through Time and Space. Therefore, their power surpass Mewtwo's with an ENORMOUS difference.
2º) Pal, seriously, think about it! During his time fighting for Giovanni, he was fighting Pokemon from regular Pokemon trainers looking for a Gym's badge, and the trainers that arrived to his island were around that same level. Against Pokemon of such trainer's level, they are no match for Mewtwo, clearly. But we are talking about Pokemon trained by members of the Elite 4 and Champions. That's a completely different level! Back in Hoenn, Lance's Red Gyarados was able to match his Hyper Beam with Kyogre's Hyper Beam. Lance's Gyarados is clearly stronger than the Gyarados trained by the guy who reached Mewtwo's island, so Mewtwo wouldn't have it so easy to defeat a Gyarados of such level.
3º) TRio is completely different from the Main Team Rocket. Even if the criminal organization was defeated, they will keep operating as the "Team Rocket" because they don't know to do anything else. It's just like some old member from Teams Magma, Aqua and Galaxy that appeared in the anime. After their organizations were dissolved, they kept being criminals, just like the disguise guy from Team Magma who used a Ditto. Besides, even if Team Rocket was defeated this Generation, they could return in the next one somehow, using the plot from the games of Gen I and II. In Gen I, Team Rocket was defeated and disbanded, while in Gen II, they tried to reband it. So, Team Rocket would be taken DOWN not OUT