-Because it is outclassed by other Electric types such as Zapdos, Magnezone.
-It's base stats is very low.
-It's movepool is very bad. It doesn't have any good move.
-If it is in level 100, still it is outclassed by others.
-Very weak Pokemon, can't hit much.
-Most times it struggles to defeat a Pokemon.
You have seen it is very strong, right? It easily defeated Alain' s Metagross, Tyranitar and a lot of Pokemon. And it's single thunderbolt always blasts off team Rocket. Actually, anime is illogical. It doesn't follow the games. Level and Stats aren't existed in the anime. It just shows how to love a Pokemon, take care of them. So, children will start playing Pokemon. Yeah, Pikachu is so strong in the anime, but anime and games is not same.
Can a water beat it? It doesn't make much sense. It depends on their moveset. If this Pokemon is a Magikarp, then Pikachu can beat it. But if this Pokemon is Quagsire, then Pikachu will struggle to beat it.
"If something that has a weakness to electric can beat it than that can be a proven weakness to pikachu."
Can you give a moveset of Pikachu? Then I can show you how easily a water type can defeat it. I showed you, Vaporeon can easily beat Pikachu. It depends on their moveset, but most times, Pikachu will lose due to its mediocre stats and bad movepool .