Quite simply, be able to have more than one couple of Pokemon be able to breed at once. Maybe have it set up kind of like the PC, where you have a certain amount of slots and each slot holds one couple?
Definitely needs to be added, it's not a huge inconvenience, but I agree.
Otherwise, I had an idea about Pokemon that go into the daycare together will gain higher stats during double battles, but it's a little out there. I'd definitely like to see some breed only Pokemon, that you can only get at random, it'd be annoying, but maybe give them higher stats? Also, I think being able to have Pokemon produce random eggs with other Pokemon if you haven't placed two Pokemon in the daycare. For example, I put in a Froakie, and the game will breed Froakie with random Pokemon (Clocked based events.) If no Pokemon was in the same egg group as Froakie during that time, I wouldn't get any eggs. The only flaw with this idea is that you'd be able to breed any Pokemon at will, instead of having to have two (or Ditto.), but most Pokemon aren't that rare anyways, and this could be solved by moving the daycare farther away from the starting town, because no one uses it for training anyways. Additionally, it would be cool to have a HUGE daycare center in this region (Again, placed in a later area.) where you could enter, and chat with trainers, have battles, play with Pokemon, and maybe have some mini games, as well as find special items like berries at certain times, or based on what Pokemon you have in the daycare, and maybe even have a Safari Zone type area, separate from the daycare, of course. (It's been awhile since we've seen one of those.) Maybe your Pokemon could learn different moves based on how much and when you interact with them in the daycare, and if you entered the daycare, you would be notified when your Pokemon is leveling up, wants to learn a new move, etc. What if new Pokemon in the region had different evolutions (Similar to Eevee.) that where determined by your interaction with them in the daycare... This may sound really unlikely, but we know very little yet, who knows, and with the whole grand, gigantic, theme of things that we've seen so far in X and Y, it might be a possibility.
Whatever, let me know what you think :D I kinda wrote a book here so...