Vulpixy's idea is probably one of the most practical ways you can do it, but still has the issue of causing you to shift your entire Gen 1 binder section every time a Charizard or Pikachu comes out -__-. You're really going to have that problem no matter how you organize it as long as your collection is still expanding... but here are some ideas to consider:
1. Do an "official" Pokedex binder that only contains one card for each Pokemon, and store the additional cards else where. You could display your favorite card for each Pokemon in the binder, and easily switch it out if a new card comes out that you like better. This would prevent you from having to constantly shift cards, but has the downside of not being able to view all the cards you have for that Pokemon. Additionally, I think storing cards outside of a binder increases the likelihood of damage, so you'd probably want to consider still storing the extras in a separate binder.
2. Expanding on the idea above, you could give popular Pokemon, such as Pikachu and Charizard, or some of your favorite Pokemon, some additional card slots. Give them as many spots in your "Pokedex" as cards you currently own (or wish to own), and then make that the set amount you display (such as 9 Pikachus or 18 Vulpix or 3 ... whatever). Then, same as the previous idea, if you get a new card you like better, you just switch out one of the ones currently you in your binder. This way you would have more options to switch from for Pokemon you really like or that get a variety of cards.
OR
3. The least visibly appealing idea, leave blank spaces after popular Pokemon (or popular evolution lines) to reduce the amount of shifting that occurs. As an example, lets look at the Pikachu evolution line. We can pretty safely assume that there will always be a consistently substantial amount of Pikachu cards released if you're including promos, a decent amount of Raichus, and Pichu doesn't matter cause he's a later Pokedex number. Keeping how often this evolution section gets additional cards (and thus causes shifts in your binder), you can create an "evolution group" of sorts, that has your Pikachus, followed by your Raichus, BUT at the end of your Raichus you leave the rest of the page empty (or fill it with electric energy cards or card sleeves or something to keep it visually interesting... ). This would allow a new card to come out in the Pikachu evolution line, without requiring you to shift every single card for every single Pokemon that follows it. Since you already have gaps, you could even just start Pikachu on a new page regardless of where Arbok is on the last page... giving Pokemon before Pikachu in the Pokedex with prints ranging from low to average room to shift without specifically saving space for them. Looking back at this paragraph, that actually sounds like a lot of work to decide which cards would get sections and which wouldn't. I guess you could always start at sectioning cards off that are guaranteed infinite printing (Mewtwo, Eeveelutions as additional examples), and then if you come across a Pokemon that seems to be taking up a lot of space and causing a lot of shifts, just separate it from the pages around it and make it its own section.
So, uh, as a summary... idea 1 is probably your easiest option, and idea 3 is an attempt to make your life easier if your REALLY want to show every card for each Pokemon. Also, idea 3 would probably work best if you also separated into different binders/dividers by generation... or something.
