This is probably known, but it's annoying me quite often:
- The Pokedex button on the forum links to B/W Pokedex, whereas it would make more sense to have it link towards X/Y Pokedex.

Other things that would be handy:
- A breeding chance calculator on Serebii, such as this one: http://destinyknot.tk/
- A Legendary encounter calculator. Same as above, but used to calculate how much chance you have to encounter a 5IV Groudon through soft-resets etc.
- Not sure how much work this is, but it would be nice if there was an Egg Move calculator. If you aren't breeding within the field group it can be very puzzling to figure out what breeding chain you have to go through in order to get all desired egg moves on your Pokemon. If a tool would simply show you the quickest path, that could make things a bit easier.