ORIGINAL: MinnFlyer
From what I have seen on these forums, JR/Spektrum seem to be easier to program, but a lot of people have had system problems.
I use a DX-7 and I actually like the Futaba programming better. Maybe it is because I started out with Futaba 72MHz radios and I got used to the way they do things.
One good thing about Spektrum/JR is the model match feature.
Still, I think I may give Futaba another look the next time I move up in radio. When I fly someones airplane with a Futaba transmitter, I just like the layout and feel a little better.
I don't think any of them are bad though; just comes down to personal preference and features you like most.