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My favorite was Archeops, it had ridiculous attack power and very good special attack and speed. Its defenses are horrible but I don't think I ever died with it because of its great offense and speed. Samurott is close behind though.
I chose the plume fossil because I needed a pokemon who could fly and archen was one of my choices so I decided to get him. Also I started with oshawott, so i didn't need another water pokemon for my team.
I hate Magikarp because they don't give out much exp. I hate battling Wobuffet because they have good defense and destiny bond is annoying. I hate Blissey too because one on leaf green had kept using minimize and it already has a lot of HP, so it was a long battle.
All of that isn't necessary, you might wanna be at about level 55 to face them, but on my diamond my team to beat the E4 was:
Empoleon
Luxray
Staraptor
Rampardos
Garchomp
and some other pokemon I can't remember right now, and they were all lv. 50. The E4 still didn't give me that much trouble.
My favorite is when I go to Vermillion City. The music brings back so many memories of my Blue version it sometimes make me sad that you can't go back in time.
The best choice would probably be Totodile. I'm not saying that because I love all water starters, but mainly because it doesn't have any weaknesses against gym leaders in johto and it learns ice fang which can give you an advantage against Claire and Lance. In kanto it only has two weaknesses...
This hasn't happened to me in ages, but if it does, it won't bother me because I save the game frequently. (I think I save this much because I have slight OCD).
I hate the dude's name. If I were him I would never visit my mom on the game for a dreadful name such as Hilbert. (I'm sorry if that's actually someone's name and they read this.)