Actually, that depends upon which JR system you're considering. If you're talking about the JR/Spektrum DSM and DSM2 kit from the past, then what Pete says is really quite true. HOWEVER, JR has recently introduced their newer DMSS format system which has fixed nearly all of those concerns.
I have flown a JR XG-11 DMSS system from the time DMSS was introduced up until just recently when I finally made the switch to UHF. In fact, I still have a DMSS hex that I've no plans for converting. The DMSS receivers are all diversity, they bind in miliseconds, they handshake on power-up equally as fast, they also reacquire just as quickly. You can get DMSS radios from 6 channels to 14...whatever you want (and your wallet can afford).
Not to mention, I have routinely flown them 2km and further away without control dropouts.
The downside is that the receivers in the past have been a little pricey (11 chan rcvr ran about $125) However, I have seen clone DMSS rcvrs on HobbyKing lately much lower. So I suspect that JR may be drastically reducing their pricing very soon.
Futaba kit is just as good, don't get me wrong. But don't let your impressions of the older JR stuff cloud your thinking on the new stuff. JR has come a long way.
Right now....I'd say go look at the radios and receivers and choose the one that suits YOU better. Either way....I think you'll be happy. Especially as you are already a JR kind of guy.
....sT