I too have this same issue. It especially shows up when you decide to activate other Ouya Controllers. It however does not effect the PS3 controllers connected. Currently a bluetooth RSSI is up and work in progress in measuring the strength of the controllers and console.

However, if you want to try some things right away you can hard-line your Ouya as plugging in a network jack will disable one half of the functions on the wi-fi/bluetooth chip. It should give bluetooth total control over the antenna in the Ouya. Some people report tipping their Ouya worked for them. It did not for me.

If you are unable to hard-line your Ouya. Since bluetooth is on the same 2.4Ghz range that changing the wi-fi broadcast channel on your router may help with lag issues as you are moving around the microwave signal enough for the bluetooth to operate better.

Some people believed the v0.0103 retail launch released controllers were problematic and that controllers above this release worked a lot better. To check this go to MANAGE > SYSTEM > ADVANCED > Bluetooth > Use the mousepad to tap the settings icon that is on the right hand side to your Ouya Controller connected . And then with the same mouse-pad tap the Firmware version to reveal what firmware you have.

The variance of this problem could deal with the environment the Ouya is in which could indicate why some users on the forum have zero problems with their Ouya while others had non-stop problems regardless how many controllers they try. There could be a relation between how dense the background microwave radiation noise from routers within your community versus the Ouyas performance but it's all speculation.

That's about all that can be done without going down the road of insanity with soldering irons and/or dissassembly of the Ouyas case to see if performance improves while the Ouya is naked.