I have an ebow, which I used to use religiously but haven't used as much lately, but I've never played a guitar with a sustainer. So what I'm saying here may be completely wrong!
I think the biggest difference between the sustainer & ebow is that the ebow only works on one string at a time, while the sustainer can work across all 6 (7) strings at once.
That said, I think there would be some different technique required for each. I think the sustainer would require you to mute all the strings but the ones you want to sound, which could take some getting used
to. The ebow probably provides greater versatility, because you can hold it at different locations on the string, fade in & out by moving on and off the string, and even sweep across strings with it, but of course, the downside is that it only works on one string at a time.
--B