Yeah, as KA said, figuring out the kind of team you want to use is the first step. In VGC which is a doubles format, a lot of teams are based off of a single idea, and they use a lot of pokemon that revolve around it. This is different than singles where you want your team to be balanced and where diversity is a lot more prevalent. (Diversity is good in VGC, don't get me wrong, but you don't generally strive to achieve it like you would in singles.) In VGC, it's a lot easier to revolve teams around ideas like Rain, Trick Room, or Tailwind.
After you figure out what you want to build your team around, it becomes a lot easier selecting the pokemon you want to use. You'll want pokemon that both support your team's purpose while keeping other teams in the VGC meta in check. For example, if you're using a team based around Rain Dance, the pokemon you want to add to your team become a very select few. You'll want some of the pokemon to exploit rain, and you'll want others to check the rest of the metagame, but you can eliminate pokemon that rain hinders.
For example, Tyranitar. It's a great pokemon in the VGC metagame because it sets up sand, it checks a lot of threats (like Cresselia), and it's bulky and powerful. But, Tyranitar would severely hinder a rain team from doing well because it sets up weather of its own, so you know that you obviously don't want to use Tyranitar. This is an obvious example, but you can eliminate several other popular VGC pokemon like Heatran, Ninetales, Zapdos, and others because they either hinder your rain team or do not benefit from having rain up. Instead you can look at other threats like Ludicolo, Kingdra, or Scizor because they benefit from having rain up, and they can also do serious damage to opposing teams.
I know that I used examples from older formats, but the process still applies for X and Y. Get an idea of what you want to build your team around first, and then select pokemon that either benefit from or support your team while checking the rest of the metagame. I hope I helped, good luck with your teambuilding!