I have been playing more and it is clear that until I reach colony 6, I will remain a terrible player because that is just how I play these things. I just got done fighting against the Fat Metal Face (I can't be bother to find his actual name), and so far the only reason I am surviving is I have a tendency to explore. I don't have anything to put into slots, I have yet to do a side quest and I am chillin' at level 22. I thought it was hilariously funny when the tutorial mentioned important items for future quests XD
The button configuration thing is an old habits die hard thing. I could never play the Megaman Anniversary collection because the jump and fire button were switched with no way to change them. After playing for hours I never adapted to a simple two button switch on a two button game. Even this far into the game (7-8 hours) I still hit the wrong buttons in the menus. It isn't going to change.
I understand what you are saying when it comes to the item mapping but I still think giant squares with no information until you go over it is bad in comparison to a list style where names, #of slots, key stats for the item (attack power for weapons, phys/ether defense for armor) can easily be displayed. You can't really group but I still think a list works better.
At this point the ONLY attack I use is the back attack-a-mattack-a-majig. Maybe map an a key attack/art to a button instead and you can bring up the menu for other situations.
Maybe I said this stuff isn't a deal breaker but it is a big of an annoyance because I think it could have all been designed much better. I am sure I will eventually get around to doing some quests and doing other stuff but so far it has not been necessary and I have yet to get bored to the point where I want to check it out.
I also totally agree with your assessment that it is awesome that you practically immediately get to explore this huge world (although those level 80 monsters casually walking around do scare me) instead of waiting till practically the end of the game.