You get used to the shifting. People say "It gets better as the bike breaks in," but to be honest I'm not sure it really has for me, I've just gotten more deliberate and precise. It's not like a Japanese bike, where you always know exactly what will happen when you move your foot up or down.
The RE is a bike where you have to learn its quirks and then live with them. It was my first motorcycle so I think of that as normal, and then when I ride a more precise bike (such as, even, my 101cc SYM Symba, which is practically a scooter) I'm amazed at how different the experience is. But not better, just different.