Don’t rank them by which is your favorite (otherwise this list would look very different for me), but by which ones you think have the most significant legacy.
My list:
1. Base Set - I’m just including 1st Edition/Shadowless/Unlimited all in one. This one is obvious. I don’t think you’ll find a kid who grew up in the '90s who didn’t own Base Set cards at some point. This is also the set that cross-collectors go after. And, most importantly, it was the first set in the hobby. Ironically enough, it probably had some of the weakest artwork, but there is no doubt Base Set tops the list.
2. Neo Destiny - Pokemon was on its way downhill at the time, but now it seems like people seek out complete Neo Destiny sets more than any other non-Base Set set. Beautiful artwork. Eight Shining cards. The first and only set to feature Light Pokemon. The last WOTC set (key word: WOTC) to feature Dark Pokemon. The last WOTC set to have the original card template. This one has it all.
3. Jungle - I think a legitimate argument can be made for Jungle getting the No. 2 spot. Rookie cards for the Eeveelutions and Snorlax, different-looking artwork and a continuation of the original 150 (why wasn’t Mew included in English Fossil again?) Pokemon. Carries an incredible nostalgia factor.
4. Fossil - Fossil always seemed like an extension of Jungle to me with the similar knockout artwork from Himeno. What gives Fossil a serious argument over Jungle, however, is that Dragonite was the most popular card from both sets. Outside of the 1st Edition Base Set holos, this is probably the most popular set card in the hobby. Also, significant rookie cards for Articuno, Moltres, Gengar, etc., and this set completed the original 150 (again, where the heck was Mew, English?)
5. Skyridge - No one cared about this set when it was released in 2003. I’m also pretty sure no one cared about it until the boom of 2016. But now, Skyridge is viewed very differently. The price of sealed product from this set has soared to insane levels, and it was the last WOTC set ever printed. Incredible artwork helps its case. Some would probably argue it should be higher on this list.
6. Neo Genesis - The introduction to the Gen. 2 Pokemon. I have always kind of considered this the “Base Set” of the Gold/Silver era, because a lot of the artwork is just Sugimori stock art plopped on to a bland background. To me, this set has, by far, the weakest artwork of the Neo era, particularly for the holos. Still, it was the first Gen. 2 set, and it has the Typhlosion 17 and rookie Lugia, which are easily two of the most sought-after set cards in the hobby.
7. Neo Revelation - Neo Destiny may have popularized Shining cards, but Neo Revelation introduced them, and I like the artworks for Shining Gyarados and Shining Magikarp significantly more than most of the Neo Destiny Shinings (save for Shining Raichu). This is probably one of my top-three favorite sets as a whole for Houndoom alone.
8. Team Rocket - Probably the most affordable WOTC set, right? There’s a reason for that: a lot of people weren’t/aren’t huge fans of it. I personally love it. It was the last WOTC set I collected as a kid before Pokemon cards fell out of favor with me, and it has some incredible artwork. Plus, it was the introduction to Dark Pokemon. However, there is no doubting that this is low on the totem pole of WOTC sets, which is probably because a.) it was the first set that didn’t have rookie cards, and b.) most of the holos featured species of unpopular Pokemon (Vileplume, Magneton, Slowbro, Arbok, Weezing, Hypno, etc.). Not even Dark Charizard could save it from that.
9. Neo Discovery - The red-headed stepchild of the Neo era, which is a shame because it’s actually probably my favorite Neo set. I actually think Neo Discovery may have had the best artwork in the history of the hobby. Not even just the holos; I’m talking about the non-holos. We are talking about phenomenal art here. Also had Espeon and Umbreon’s rookie cards. Still, because Neo Discovery wasn’t the first Neo set and didn’t have any Shining cards, it’s kind of caught in no-man’s land and is almost certainly the least desirable of the Neo sets from a collector’s standpoint.
10. Gym Challenge - To me, the Gym sets were actually the lowest point of the WOTC era from a creativity standpoint, and I know a lot of other people agree. I was never a fan of the whole “X’s Pokemon” thing. Dark Pokemon were even weird at first, but I feel like having a person’s name in front of the Pokemon took that to another level. But this set does have Blaine’s Charizard (which may very well be my least favorite WOTC Charizard card), Blaine’s Arcanine and Erika’s Venusaur, so that gives it some staying power.
11. Gym Heroes - This might be the only WOTC set where there isn’t a standout card. Is it Blaine’s Moltres? Sabrina’s Gengar? Erika’s Dragonair (which isn’t even a fully-evolved Pokemon)? This is just a really weak set, both from a collector’s point of view and from just looking at the species and artwork.
12. Aquapolis - It was tough deciding between Aquapolis and Expedition for this spot, but Aquapolis takes the cake because it introduced Crystal cards. This is actually probably my favorite eSeries set, as the artwork is simply beautiful. But yeah. It will never be Skyridge, because it wasn’t the last WOTC set, and a whole lot of people did not like the eSeries.
13. Expedition - The introduction to the eSeries. It’s probably the most polarizing set in the WOTC era for that reason, as it represented a drastic shift in card style and template. I personally love the artwork here, but for most people, Expedition is forgettable, which is why some of these cards are absurdly cheap.
14. Legendary Collection - Yeah, the reverse holos are cool and unique, but let’s be honest: this is basically Base Set 3, and I think most people would agree regardless of the exorbitant price of sealed product.
15. Base Set 2 - Need I say more?