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My favorite would have to be Cloyster or Gyarados, with Tentacruel, Lapras and Blastoise close behind. To be honest though, there isn't really a water pokemon I dislike in the original generation.
Gyarados, Golduck and Poliwhirl. Probably. I love Staryu too, but in the games I mostly use the former three. Their designs and attacks and power is great imo. I used to like Poliwhirl and its family the most, but Gyarados and Golduck grew on me. And Wartortle deserves a mentioning, not because it's the greatest thing ever but because it looks cool.
Staryu/Starmie. They're one of my top 5 favorite Pokemon. I think Starmie has a nice typing and with that came a pretty wide move pool... and pretty good stats. Kinda makes it fun to use since you can teach it a variety of moves each time you use it and it can actually hold its own.