Not bad. Still kinda meh that it's universal and not tied to games.

Because developers want to force us to press the buttons they want us to press. I can't tell you how frustrating it was playing the early MGS games and having to use the O button instead of the X button.

That's not the case on ps4. You can set the buttons to whatever you like.  Read the posts above. 

That is the standard button layout in Japan. Developers were just to lazy to change it for western release. Also Nintendo does this for their consoles in the west as well. A button (confirmation) on Nintendo controllers is B button (cancel) on Xbox controllers. 

I know but it's universial.

Yeah, I remember reading that it was cultural but it's still a pain when you are accidently pressing "go" and it's actually "back" you know? 

There are some games that have full button-mapping, though I've only really seen it in Racing games tbh, Project Cars etc.

Like has been posted you can change the controls universally, though this won't change button prompts in games.

I can't even imagine trying to play the old Mega Man X games without the ability to remap Dash to R. Thankfully I've encountered few games have come out since that really demand remapping. (Flinthook is one; still not sure why they assigned two abilities you probably want to use together to L1 and L2, meanwhile completely not using R1.)

Also speedrunning super metroid without remapping weapon select to Y is a pain in the ass. 

Probably for the same reason there's not many other options either. I'm not sure what that reason is though. A part must be that it's extra work, and they don't think it's worth the effort. PC people are generally more demanding so the devs do it there (usually), but console people seem to be happy enough with what they get. Also, a keyboard is not exactly greatly shaped for controlling games, so it's more important to let people change their key bindings. A controller, on the other hand, is much easier to get right because it fits in hands pretty well and every button is easily reachable at all times.