I think mine will echo a lot of what has alreadly been said, but its such a fun topic I wanted to make my own! I’ll give reasoning for my more out there picks:
EX Ruby Sapphire: Torchic, Mudkip, Treecko
EX Sandstorm: Armaldo, Cradily
EX Dragon: Latios, Latias
EX TMTA: Groudon, Kyogre
EX Hidden legends: Regi Trio
EX FRLG: Venusaur, Charizard, Blastoise,
EX TRR: Mewtwo, Meowth
EX Deoxys: Deoxys(All forms)
-Though 4 were never in one set it just makes too much sense to not have them all here and imagine a complete set 
EX Emerald: Rayquaza, Milotic, Seviper
-Rayquaza for obvious reasons, Milotic as the ace of Wallace who is the champion in emerald, and Seviper to represent the Battle Frontier an iconic addition to the game where the battle pike is shaped like a Seviper
EX Unseen Forces: Meganium, Typhlosion, Feraligatr
EX Delta Species: Porygon, Ditto, Metagross
-The Delta Species saga of sets has my favorite lore from the tcg and I wanted to reflect that through my GS choices. The lore behind the Delta Species(Holon Research Tower) set is that a group of scientist set up a big tower in a region known as Holon in an attempt to track down Mew. Once the machine is turned on it lets out these magnetic waves that begin to distort the Pokemon in the surrounding area thus making the delta species Pokémon. So I wanted to display that scientific element in my picks. Porygon for the reason of being man made(plus a fantastic shiny), Ditto for the reason of he can change into any pokemon thus changing type reflecting the Delta Species Pokemon plus if you subscribe to the theory of Ditto being a failed Mew clone then its an experiment gone wrong much like the Holon tower itself, and Metagross with its super computer like intelligence no doubt fits the vibe of this set, plus a gen 3 psuedo is a great addition to the GSs regardless.
EX Legend Maker: Celebi, Jirachi
EX Holon Phantoms: Banette, Dusclops, Gengar
EX Crystal Guardians: Gardevoir, Dragonair, Sableye
-I have always associated Crystal Guardians with this fancy dignified esthetic. The main 2 cards to me have always been Jirachi and Delcatty ex so as such to fit that theme I think Gardevoir would make an amazing GS(plus another great shiny), Dragonair for the same reason. We have seen in the past pre evolutions aren’t excluded from gold stars so I say go for it. Added bonus with the gem crystal on its head too. Sableye really only fits in the naming convention of the set, but I love the little goblin so I couldn’t not.
EX Dragon Frontiers: Mew, Salamence
-So I kept Mew here because I always thought that they stuck the landing with this addition to the set. Its not a dragon or even draconic like charizard its GS counterpart, but in terms of the lore it fits perfectly. Dragon Frontiers is set in the far reaches of Holon where naturally occurring DS Pokemon dwell as seen by them not having a secondary metal typing which all effected by the waves have. I think it fits perfectly that Mew was rightly tracked to Holon and even a DS Pokémon, but just off the horizon of the the scientists research thus making the quest for the elusive Mew continue!
EX Power Keepers: Blaziken, Sceptile, and Swampert
-The set is all about the Pokemon League of Ruby and Sapphire and I think it is showcased pretty well so I think a fun way to add onto that theme while also being a grea close to the era is to do the final forms of the gen 3 starters. A set of mons that most certainly many trainers had at least one of heading into the league on there adventure through Hoenn.
