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Are there any hints by mixing both types of APs on one controller?
Could clients use draft-n speed as long 1242AG APs are on the same controller?
You can disable certain data rates on each specific AP. So for your 802.11n APs, disable the B and G rates for a pure N radio. If nothing else, I'd highly recommend disabling B data rates.
There's no harm is using a mix of APs on a controller, though. They don't negatively affect each other's throughput.