I was slightly concerned about the popularity aspect of it for the same reasons as you, but looking at previous handsets/tabs in the "Z" line, I'm not sure it will be a problem. Plus, from what I can see, Sony appear to be pretty good with source code so it might not be too much of an issue.
A lot of the reasons I've had for rooting/ROMing in the past are now moot anyway (Titanium, messing about with themes etc), you have helium for backups now and if the the Experia Z is anything to go by, the UI on this thing will be amazing.
I think there's enough about this on stock to keep me going for a while.
I say that now obviously, but we'll see....