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I would mainly focus on fixing the battle mechanic glitches such as the 1/256 miss chance, focus energy not working, etc. I would make freeze work like it does now so it's not an instant kill. I would make trapping moves work like they do now. I would add in shadow ball and dragon breath so that dragon and ghost are actual types. I would increase twinneedle to 40 base power and let every bug type learn it so that bug is an actual type too. I would increase wing attack to 60 base power like in gen 2 onwards. I would make karate chop a fighting attack like in gen 2 onwards. That's it really.
Also I would leave in the cool useful glitches like missingno.