Firstly, I don't know what your process for getting a re-entry is, but as far as I'm concerned it's absolutely no hassle whatsoever. I just get one automatically as part of the yearly extension process.
Even if I didn't, it would still only be a simple five minute process at my nearest Immigration office (admittedly I'm lucky in that it's only five minutes from my house).
Maybe I'm not understanding the situation correctly with the OP or maybe they aren't (I'm not sure) but for me the re-entry permit is highly useful if not absolutely critical.
Without a re-entry permit, if you're on a yearly extension of permission to stay (and I don't know why else you'd even be thinking about one) you would lose your extension - as others have pointed out it would be automatically voided.
On returning, would only get a 30-day visa exempt entry. Then if you wanted to stay long-term again, it would mean starting again from scratch by converting to an O visa - which to me represents a much bigger hassle than getting a simple re-entry permit before leaving.
The scrapping of the TM6 and lack of need to report on returning have nothing at all to do with the reasons for getting a re-entry permit, which is to preserve the validity of your permission to stay.
Note: For some reason, my replies keep getting changed to bold text half way through. Not sure why. I could go back and retype but it doesn't seem worth the effort.