Mega charizard x has been around for awhile so it's not like they pulled it out of their butts (and ash-greninja was in there too so it was pretty even what with the type switch eliminating that pesky water-type weakness).
Pikachu had crappy endurance so of course taking solid hits from THREE DIFFERENT POKEMON was too much for it regardless of level. Greninja could've come out of the gate with an advantage if it had used water shurikan instead of cut when rain dance was still active (that move one-shot bisharp for crying out loud! Did Ash have a brain fart there or was it just him hating it when things aren't a challenge? Meh whatever setup for a good fight).
The fight there was certainly better than the league before that (losing to a trainer who brought five pokemon instead of six?!? Seriously?!? And that guy didn't even win the league anyways!) or the league before that one (a trainer who had not one but TWO legendaries) The fighting was properly tough, Ash put up a good showing knocking the trainer down to his last (and best) pokemon and whipping out an evolution that wasn't supposed to be around until the next league.
The other trainer had been taking on mega-evolutions with his own before Ash had hit the fourth gym (giving him a craptop of experience), and pretty much had Ash beat strategy wise (spirit wins gym battles strategy wins leagues).
Overall though the only reason Ash keeps losing is that he keeps going after new friendships and resetting his team rather than maintainingand cultivating his existing ones. I'm pretty positive if Ash had gone back and used some of his pokemon from the previous leagues...he would've won that fight because the experience his pokemon would've had would trump the experience from the other team....I have to admit that Ash IS learning though. Aside from using cut instead of rain dance I didn't see too many strategic mistakes on his part.