Hmm...
Well, the first thing that comes out of my mind of when Ash's Pikachu demonstrated tremendous power was during the episode "On a Wingull and a Prayer" (season 6). Remember when Ash and friends along with Captain Briney was giving chase to that Team Aqua guy on sea? During that one, Pikachu nearly completely demolished the large lump of rock they called a "mountain". Whether it was one or not, that was a really big stone to destory in one shot.
There's plenty more evidence where Pikachu shows off its power, such as being able to actually stand up to a lot of the legendaries it meets up with for the first few minutes. I doubt a normal Pikachu, even with enhanced abilities, could stop an attack from Kyogre.
I bet Team Rocket sees this, and knows what potential the yellow mouse has. Though it does make me wonder why they have to use flawed giant machines to do the job... (and how much money Giovanni is willing to put up for them)
...
Honestly, I think Ash's Pikachu is holding out on all of us. It just doesn't want to destroy everything in its path... (I know there's no evidence on this; it's called an opinion!)