Are far as modifications go, we should also think about ways to make evolution cards more viable in the format (nerfing energy removal stuff is a good start) and make overused Pokemon less viable while making underused ones for viable.
Here are some ideas for the base set.
Blastoise - When you attach an energy using the power, it receives 1 damage counter.
Chansey - Requires 2 energy to retreat.
Charizard - Reduce retreat cost to 2.
Gyarados - I would look into giving this card a complete overhaul. Perhaps look into the Gyarados from other sets for ideas, like adding the Flame Vapor power from the Ecard one, reducing retreat to 2, and giving Bubblebeam 10 extra damage.
Hitmonchan - Reduce HP to 60
Machamp - Strikes back does 20 damage instead of 10.
Magneton - 80 HP, and only 2 lightning energy for Thunder Wave.
Poliwrath - Reduce retreat cost to 2, Whirlpool to 3 energy requirement and reduce to 30 damage.
Raichu - Reduce Agility to 2 colorless energy only and change Thunder to 3 lightning energy requirement.
Beedrill - Reduce Twineedle to 2 energy requirement.
Dugtrio - Reduce retreat cost to 1, change Slash energy requirement to 3 colorless energy, and change earthquake’s energy requirement to 2 fighting and 2 colorless energy.
Electabuzz - Reduce HP to 60.
Dewgong - Increase HP to 100.
Farfetch’s - Increase HP to 60 and reduce retreat cost to 0.
Jynx - Change Meditate energy requirement to 2 psychic energy and reduce damage to 10+.
Kadabra - Reduce retreat cost to 1 or 2.
Machoke - Reduce retreat cost to 2 and change Karate chop damage to 60.
Nidorino - reduce Horn drill energy cost to 2 grass and 1 colorless energy.
Porygon - Increase HP to 50 or 60.
Raticate - Reduce retreat cost to 0.
Gastly - No coin flip requirement for Sleeping Gas.
Pidgey - Reduce Whirlwind energy requirement to 1 colorless energy.
Starmie - Reduce retreat cost to 0, increase star freeze damage to 30, increase HP to 70.
Tangela - Increase HP to 70, reduce Poisonpowder requirement to 2 grass energy and change Bind requirement to 2 colorless energy.
Voltorb - Reduce retreat cost to 0.
Pokemon Breeder - Can be used to evolve a basic pokemon into stage 1 as well, even if it was just played this turn.
Pluspower - only 1 can be attached to your pokemon per turn.
Pokedex - You may add 1 pokemon card there, then rearrange the other 4.
Gust of Wind - Change to supporter card.