I only see upgrades in the fw update. The bluetooth app works like a charm for me with my aged iphone 6, and pairs instantly. Very handy, I've seen loads of sales gimmicks but this is definitely not one of those. Disabling USB needs some explanation, but it doesn't bother me the least bit, and heard it'll be revived in the next updates. The menu controls are now greatly improved with the latest updates. I'm never a fans of any brands, definitely not Onkyo's, but the Rubato ticks many boxes more than its competition, and it sounds great as long as the sound preference goes well with you. Its a matter of taste but I won't trade my Rubato for the AK Jr (I've owned one before, one of the worst buy made ever and glad they get things right with the AK70 in no time) even if I get paid for the swap.
Regarding your problem, I gotta say:
1. Of all players I've owned, only the Sony WM1 siblings would keep battery alive for DAYS even if you dun switch it off. And when the battery drains ALL players need to recharge before coming back to life, sometimes as long as 15-20 mins before any signs of revival.
2. Only a guess - given your failed attempt to reproduce the "problem" on 3.5, for the instance when your problem did occur, maybe you have just pulled out your 2.5 hearphone without actually stopping the playback first? For basically all players with a balanced output (maybe with the exception of AK), doing that on balanced would NOT automatically stop the playback, even if it does when on 3.5 SE. Even the newer Sony 4.4 output won't stop playing if you just unplug the headphones. That of cos would cos battery to go on draining and will be dead in no time.