I agree with Scotty about the SE shifter being in the way, it hasn't been a problem but it keeps me from being able to wrap my hand around the grip completely. I have gotten used to it but my finger and thumb just hang out on those long rides.
The SE seems to need about 1000 RPM's more to not feel as though it is lugging. Where my GS-SM could cruise at 3000 or so, my ST-SE needs to be at least 4000. The SE has reduced the control compared to the clutch and the fly by wire throttle has reduced it even more, nothing we can do about that.
While the SE is growing on me, it would be a hard decision if I were to get rid of both and purchase a new one, I would still lean towards the manual trans, I think, maybe. The SE works as well as a semi automatic can and is well executed in it's design, but a few more things to worry about electronics wise, some linkage falling off very occasionally, slightly more maintenance cost, early clutch failure from too low RPM's etc.
Some of the riders that have always had manual shift cars and motorcycles all their life seem to have switched to the SE and find themselves loving them more than they thought they would, myself included.
If you like to shift and feel a little more connected and you don't have too much arthritis in your hands or feet, get the SM. If your ready to take it easy and cruise and not have to put as much input into the driving, get the SE.
The SM can also work to your advantage if you don't want everyone wanting to take your baby for a spin all the time just because they can do the automatic, while your home pacing the floor hoping they keep the rev's up so the centrifugal clutch doesn't burn out. On the other hand you may want the SE to encourage them to learn to ride if that's what it takes.
They are both great in their own way, good luck, you will be happy with either.
