This is a list of things i noticed in the Mega list, as well as suggestions afterwards. I will update it as i go through all Pokemon on the list:
HP Increase/Decrease:
Gen 1
Tauros (HP Can't Increase) split 20 bonus HP into +10 Speed and +10 Attack
Gen 2
Stat increase not 100:
Gen 1
Butterfree (90), add 10 SPD
Beedrill (90), add 10 DEF
Raticate (110), remove 10 SPD
Arbok (120), remove 20 SPE
Nidoqueen (90), add 10 SPA
Nidoking (90), add 10 DEF
Gen 2
Noctowl (80), add 20 SPE
Ariados (90), add 10 SPE
Skarmory (105), remove 5 SPD
Deemed underpowered:
Gen 1
Gen 2
Deemed overpowered:
Gen 1
Mega Lapras Y (Great defensive typing, Its Defenses are really high, and Hydration means you can't Toxic it in the rain. Its Special Attack also means it can hit you hard if you setup to kill it.) Lower either of its defensive stats or edit its ability to allow Toxic on it
Gen 2
Octillery (There is no reason to reduce Octillery's Attack to so low just to buff its other stats, this just makes Octillery way overpowered) Keep attack as it is and reduce the speed by 50.
Deemed not fitting:
Gen 1
Seaking (Pure Power is for Fighting types, Huge Power is for the rest.) Use Huge Power.
Omastar (Speed increase while its shell grows heavier because of steel typing) Reduce Speed by 30 and add 10 ATK and DEF
Gen 2
Unown (Plain Sight is a weird name for an ability that makes Hidden Power better) how about Found Power?