personally, I think ubers should only be used in the game just to get through the E4+ Champion for quick money. That's one of the biggest ways to get dead rich in the game, espically if you have an amulet coin or two.
For battling, I say no ubers unless both sides have at least one (meaning in a player vs player match, the computer provides no challenge). My reasons:
1. too powerful, a level-80+ uber can take out an entire team of level 100's easily (trust me, if a level 80 non-uber can take out an entire team of level 100's, then an uber can do it easily)
2. even if the uber isn't statstically the same, they have much greater move pools to pull out an SE attack against many others
3. thanks to the abilities in R/S, ubers are now even more powerful. a Mewtwo can be a staller and slowly drain the other teams PP thanks to Pressure, and the same thing with the others.
4. an uber's stats are usually off the charts in at least one catagory, the one that they usually focus on anyway. Even then, it's not like all the others are toilet-worthy, even though Kyogre's Sp. Def is twice as high as it's Def, it can still take a beating from powerful physical attacks and wipe them out in one deft blow
