Well lets see if I can give it a try.
The first problem is that some idiots tried to make a movie version of a game that pretty much revived gaming, developed a pretty huge following and created a set of iconic characters for gamers everywhere. Also note that these characters HAVE ESTABLISHED ROLES, APPEARANCES, AND RELATIONS WITH EACH OTHER. Not to mention a relatively well known setting in the Mushroom Kingdom. Now while I mentioned that the characters have all these nice things the story is pretty bare bones. Princess is kidnapped Mario and Luigi saves her, Mario gets the shaft. Oh and for the idiots out there Bowser is the one doing the kidnapping.
So the issue arises, we have an incredibly popular property that is a lacking in the story department. What do we do? Well we can try to make a light hearted comedy that both celebrates and mocks the established canon and hope the fans will be pleased or we can try to make the movie "A serious action flick."
Sadly they went with this route that involved regular world (Never mentioned in the games) a bleak dystopic techno hell of a mushroom kingdom (Way off from actual description) they tried to make the villains menacing with plans for world domination (Of course!) They made the princess a secret princess for most of the movie (So hate that trope) and they made the brothers father and son...
To sum it up there were two big problems first of all there wasn't a substancial plot to base a movie off of, and the spirit of the game (Bright fun and fluffy) was contrary to the atmosphere that hollywood loved in the 1990s (Dark and edgy), and the second problem was when confronted with this problem they decided to go dark, screw the fans and make a conventional movie. Basically they sacrificed fan support to try to reach main stream, but they still held enough of the games conventions to make things seem odd. (I hope this post was coherent.)
Edit: These are the reasons I disliked this movie but if you enjoyed the move well you enjoy it and don't let any of these guys get you down. Sure most people might view it as bad, but I think everyone has a few movies that are generally regarded as crap that someone adores. I know I have a massive weakness for anything with zombies in it.