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I actually found futaba easier to program, more user intuative (just the 9c-all others a much worse than jr), more flexibility, and those coold little data cards (which give u more models and backup transmitter) etc.
BUT one major flaw (at least to me) is that the futaba doesn't let u see the "in and out of stick and servo", except in the old rough/approximate arrows when programming. The JR has a numerical value associated with both stick postion and servo output. IMHO.