This is what I do.
1. I go after each Pokemon's very first card, that could only be pulled from a pack. I skip over promos, deck cards etc. Some rare exceptions are made here.
2. Each Pokemon's first card must be a card from a set that is from the same generation the Pokemon debuted in (with very rare excptions, more on that later. Meaning for Bulbasaur, it has to be the Base Set card.
3. The card must be a common, uncommon or regular rare or rare holo card. No EX, LV X, delta, radiant, trainer, team rocket, owners pokemon, dark, light, full arts, IR etc. It must be a regular card.
4. If a Pokemon has more than one card from it's debut set, I always go for the highest rarity and/or the holo card (if applicable). If the same rarity (both cards from the debut set are common cards, for example), I chose the artwork I like the best.
5. No varients, regional varients. One card for each Pokemon.
This is all done to keep the look of the cards consistant. Since cards are redesigned each generation, usually anyway, I want the designs, holo patterns etc, to match for each generation, and overall the overall look of all pokedex cards to be the same
For Gen 1:
All cards are from Base Set, Jungle and Fossil. Mew's first pack pull card was from a much later 2002 set, and looks very different. So in this case, since I consider the WoTC promos its own set, I go for the Mew cards there. Cards #8 and #9 in the WoTC promo set are the same, but #9 is holo. So I went with that.
Gen 2:
All Neo era sets
Gen 3:
All Ruby and Sapphire era cards. Latios and Latias first pack pull cards, same issue as Mew, were from a much later set in Gen 4. Cant use that. So their first cards are their movie promo cards.
Gen 4:
Diamond and Pearl sets
Gen 5:
Black and White era sets
Gen 6:
X and Y era sets
Gen 7:
Sun and Moon era sets.
Gen 8:
Sword and Shield era sets. Exception here. Eternatus' first card that sorta looks like a regular card was a radiant card and the others were EX cards in its generation. It FINALLY got its first normal print rare holo card, but it was in the Gen 9 set, Surging Sparks. This is the only Pokemon that, in my binder, is using a card that was released in a later generation set. Gen 8 Pokemon with a Gen 9 card. Is what it is.
Gen 9:
All Scarlet and Violet era sets. Pecharunt's first card is also a promo card. No normal print card from a set yet. Still waiting to see if it gets one in a Scarlet and Violet set. If not, the promo will be the permanent card for it.
Doing it this way makes it feel like I've been collecting for a Pokedex set all along like I was when I was a kid....filling in each Pokemon as sets came out. Not only that, it shows the history of how cards changed from generation. Also, most Gen 5 - 9 cards in just common, uncommon and rare/rare holo variety tend to be very cheap, because those rare/rare holo cards are not the chase cards anymore. If you do it this way, the only expensive cards are really cards from gens 1-4. I recommend using a spreadsheet and using bulbapedia to determine what the first card is for each (searching the pokemons name and "(TCG)" at the end, for example Pikachu (TCG) will show all cards for Pikachu.)
Of course you can do it how you want, not sure about a game varient set. But it is relatively cheap going the route I've been going, at least for Gens 5-9. First cards for Charizard, Lugia, Umbreon, Espeon, Raikou, Entei, Suicune, Ho-Oh etc, are pricey. Lastly, the only Pokemon missing a normal print card is Hydrapple. But he's getting one in the upcoming Destined Rivals.
