I would like to suggest a few improvements to the XY Pokédex (I don't know if they've been suggested yet - I looked a bit but there's just too many pages in this thread).
1) Make a "Event Only Moves" list. All the way back to Gen III. For example, Meowth should be able to learn Petal Dance from the egg event in 2004. It doesn't have to show the exact event in "Method", just the generation it comes from. It makes it easier to know which moves it can learn in conjunction with that and if the user needs more info, he or she can find it in the Event Database.
2) Include moves from XD Purification in "Transfer Only Moves". For example, Baton Pass for Zapdos.
3) I'd also like to see moves exclusive from the Dream World as well, such as Sludge Wave Ghastly. It could also be in the Transfer Only list.
4) In some cases, the Pokémon is able to learn exclusive event or transfer only moves from multiple methods. I think there should be a "Details" page under the most current method, listing all the ways the Pokémon is able to learn the move. For example, Mewtwo is able to learn Fire Punch from the B2W2 Move Tutor, but can also learn it from the Move Tutor in Emerald, Platinum and HGSS.
5) Being able to sort the moves right there in the Pokémon pages by type, accuracy, power, PP, special effect, etc. would be awesome!
6) Much like the abilities that are not yet available, I'd like to see which shiny Pokémon cannot yet be obtained. You could put a "Shiny not available" in Celebi's page, for example.
7) Not exactly related to the Pokédex, but in the Event Database, I would like to be able to search for a specific evolutionary family instead of just a certain species. For example, when I search for Pikachu, it would be cool if it showed any Pichu events as well, since any Pichu obtained from an event could potentially evolve to a Pikachu with the same moves, OT, ID, etc.