Well, I think the Move Search Section should be updated. We should make it more like an Attack Dex (what it is called on other sites). Instead of having to type in a move, there should be a drop down where every move is listed. Once you click on the move you are looking for, a description of the move could be shown (like it does now) but also show all the Pokemon who can learn that move (break it into sections such as "By Level Up", "By TM or HM", or "By Dream World / Special").
We could also do the same for items. Have a drop down or multiple drop downs (break the items into different sections like Key Items, Hold Items, PokeBalls). Once you find and click on the item, it shows the item's description. It can also show what games the item can be found in and where in those games.
We could also do something similar with Abilities. Have a drop down that list all of the known abilities. Once you click on the one you're looking for, it can shown a description of the Ability and which Pokemon can have it (break into two sections: "Regular Ability" and "Hidden Ability.
Most other sites I visit for Pokedex info has all of these. It makes things easier when people are searching for one specific thing and what Pokemon go along with it.
I also think the Featured Pokemon Section should updated. If it were me, I would get rid of all the current ones and get someone who knows there stuff to do new ones. The info just seems way outdated because of all the new abilities, moves, and items.