IGNORING THE OBVIOUS "PLOT POWER" EXCUSE, A LOT OF THESE EXAMPLES CAN BE RATIONALIZED QUITE EASILY.
Now that I have your attention, Squirtle was one of Ash's original Pokemon, and therefore was bound to be one of the strongest he had access to at the time. Now, obviously, Electric beats Water every day of the week, but in its work with the Squirtle Squad, it puts its life in real danger every day, as opposed to relatively tame Pokemon battles. Now, which would Squirtle have a better chance of surviving: a real live fire, or a Pokemon's Thunder? Compared to the former, the latter was probably nothing.
As for Cyndaquil, there's no denying Gym Pokemon are strong, but any Pokemon that's competing in a freaking League is stronger still. Besides, A: Magneton primarily used Electric-type attacks, and B: Team Rocket cheats. It's in the job description.
Charizard would definitely have beaten Dusclops if Ash wasn't stupid enough to try Seismic Toss on a Ghost-type.
Buizel got lucky with the rain activating Swift Swim. That's all I have to say about that, other than I will concede that it was a bit too convenient.
While I agree sending out Noctowl against a Steelix was a boneheaded move, Ash has always been a bit of a maverick when it comes to type matchups. It did defeat two of Conway's Pokemon, so I'm pretty satisfied with it.
So Taillow lost a couple battles. It was still relatively new, and in its base form to boot, so I can forgive that.
My point? While wins and losses may be up to the writers, ultimately, there's a reason for each one that has significance in the development of a Pokemon's character. Calling "Plotkai" all the time is just ignorant. Some would say so is making sense of a kids' show, but I like to think the writers know what they're doing battle-wise.
I am staring to think that the writers deliberately made Torterra the fall guy because they didn't want two powerful Torterras. Paul's starter must undoubtedly be his most powerful poke'mon, and if Ash's Torterra was also shown to be a powerhouse, it might've complicated some things. Such as it would lead to a Torterra vs Torterra battle in the league, and no matter which Torterra won, it would've caused lots of criticism. So maybe they thought, just make him a loser from the start.
I just want to mention I was against Grotle evolving from the start. I would've loved to see it defeat Paul's Torterra in the League and maybe evolve upon getting that victory, but there's no changing the past.