What else is wrong with the 3DS version? Maybe I'm too early into the game, but the limitation on skill points that you're describing doesn't sound like a huge deal. (then again, I'm splitting skill points between their main weapon and their character-specific bonus)
The limitation is a-ok by me, it's just that the game was needlessly unclear on what level you needed to be at before you pass the skill point threshold it puts up. If that was more transparent I wouldn't have been irked enough to look it up, and I deliberately avoid looking up these kinds of things so this felt pretty egregious to make me check out GameFAQs for a second.
As for what else I don't like about the port, the music isn't orchestrated and is midi. I don't have a big problem with this even if the trumpets sound bad, but my main issue is with the included version of To A Vast World, the overworld theme.
Basically, I play most games with headphones on. I live with my family and I don't like bothering them during the day or waking them up at night when I play games, plus I can hear the music better.
Now, imagine someone like me having to hear the high frequency dog whistle sound that pops up at 0:37 of the video, every other damn minute of exploring the overworld. I haven't seen anyone else mention it but even though the sound only lasts for 2 seconds (about from 0:37-0:39), it makes me needlessly question if something is wrong with my ears whenever that sound comes up, and it's incredibly grating to listen to.
Everything else about this port is fine, but these couple of things have bothered me quite a bit the past few days.