My initial reaction was Neo Destiny, but part of me thinks it would feel incomplete without the other Neo sets.
I’d probably lean towards VS. It’s big enough that it could take a while to complete, and there’s a lot of variety in the artwork.
Vending is also a good choice.
Expedition.
I like how the first two generations are so well represented. There are two versions of every starter, and so many other popular Pokemon are featured. It has such phenomenal artwork, too.
1st Ed base for English. Vending for Japanese, with the Masaki cards. 
Steam Siege 
Expedition
The amount of rare variants is insane.
Sample
FPO
E3
E1 Unlimited
Matchprints
Starting now it would probably take a lifetime to achieve all of those lol
Jungle! Just because it’s peak nostalgia for me and then I can keep my childhood set plus I can collect unlimited/1st edition and no symbol 
Definitely have the nostalgia for Gen 1 but I’d have to go with a neo set, Genesis or Destiny.
no set has all my favs but would probably have to go with Aquapolis.
My favorite individual cards are all in EX era but pound for pound those last 3 WOTC sets have more to offer IMO.
If I could only collect one gen it would be Gen 3, forgoing my species collection of Tyranitars - as much as it would hurt.
1st edition Base set.
Worlds promos being a close second (if you can consider them a set)
My favorite set is Double Crisis, so I’ll go with that. Too bad it’s so small…
Greetz,
Quuador
Toss up between Jungle and Rocket for English, Vending for Japanese
I’d probably go for Skyridge overall. E series style is my favorite in terms of the card design and artwork. Aquapolis has some individual stand out cards, but I think Skyridge just barely edges it out. When it comes to anything past e series it would probably be Evolving Skies. So many good artworks in there.
Eevee Heroes for modern
Delta Species for the middle section that we can’t agree upon a name for
Jungle for vintage
Agree with those who said Vending! But on the proviso you could include every card with the same set logo - Red/Green gift set, Masaki, WHF sheet, Corocoro etc… Best set for ‘related’ cards.
Vmax Climax - though runner up, Double Crisis.
Both amazing cameo sets.
Jungle. Each card just does it for me. The holos are amazing in both Japanese and English and the set is small enough to have focus yet different enough to have variety.
I’m not sure if some promo sets are accepted as an answer, but if I have only 1 choice, I would pick a Japanese promo set like natta wake.
I wish I could be contrarian but for me its Shadowless Base Set. Nothing comes close.
Since others are cheating and including a set for English and Japanese I will also say ‘screw the rules’!
English: Skyridge. Best art for English WOTC hands down. Incredible themeing despite being composed of two separate Japanese sets. Fantastic assortment of chase cards that includes legendaries, Eeveelutions and fan favs like Gengar, Gyarados and of course, Charizard. Also has the best Crystal card E-reader layout for all English sets.
Japanese: Was really close between Vending and Vs but I have to give the edge to the latter for its immaculate theming where each gym leader’s Pokemon was drawn by a single artist. I also love how although the set features gym leaders from both Johto and Kanto that the focus is placed on the Johto leaders (and elite four members sans Koga) as the Kanto leaders already had the Gym Series sets. It is absolutely criminal that we did not receive an English version of this set but in a way that exclusivity makes Vs even more enticing to collect.
Base. Theres so many deck box variants to collect, plus demos, trainer decks, and the starter giftbox. I think total count is 42 that are known without counting gold strip decks (47 with those). Next closest set to that amount of deck box variants is Jungle (which is amazing with 20 box variants for just 2 decks).