Uber is a Pokémon deemed too powerful for normal play. OU consists of a certain amount of Pokémon that are most commonly used but are balanced out by other Pokémon in the same tier. When a Pokémon dominates the metagame to the point where it's making the metagame worse rather than better it'll get put to a suspect test. This consists of 'laddering', those who score a certain amount of points (not quite points but rather a ranking of such, hard to describe) are able to vote on whether they want to keep the Pokémon or not. Other times a council (a group of people who head the tier) vote and decide between themselves.
You can make a team of what you like but it won't get you far competitively. The best thing to do is to pick a tier (even ubers is a tier - there's no Pokémon that can't really be used competitively except mega rayquaza - which is completely banned) with Pokémon you like and play in that.
If you're interested in battling competitively (on Pokémon Showdown) the best thing to do is to read up on some of Smogon's guides (
www.smogon.com). Smogon is the competitive battling authority and decide the tiers.
Smogon's webzine has useful guides (
http://www.smogon.com/articles/) it also has a strategy pokedex (
http://www.smogon.com/dex/) which will show you tiers as well as strategies. Best thing to start out with is to jump on PokeCommunitys battle server and do 'random battles' it'll help you learn the basics of competitive.
If you're participating in official Pokémon tournaments on your 3DS (which you're not, but still mentioning anyway) you should look at Nugget Bridge.
Good luck!
Oh and if you're playing for fun, check out other metagames (should be on PS, might not be played as much on PC so maybe go to the main server for that), there might be something you like there.
