This subject is getting discussed in a lot of game threads, which scatters the discussion so I thought I'd start a thread just for discussing this everlasting discussion.
I'll just start with a known fact. There is no such thing as a Valley official. There are only NCAA-certified officials. I assume they're certified. The officials work as many games in a week as they can schedule, so they're officiating multiple conferences. The Valley upped its pay scale a few years ago and now mostly shares officials who work at and above the CUSA, MWC levels. The less experienced officials and experienced officials with weak reviews tend to work mainly conferences below that level. The Valley employs officials from the upper echelon of D1 officials.
So, why are MVC officials so bad when they're officiating our games? They're probably about the same, but there's not the emotional attachment when a Valley fan watches a B12 or B1G game, so fewer questionable calls are noticed.
There are two factors that affect the officiating. One is the conference. The conference may have guidelines, areas of emphasis, or enforcement goals that differ from other conferences. The conference may request (or possibly require) officials to call MVC games diferently than those officials call games in other conferences.
The second thing that affects the way games are called is the way games are played. The Valley plays a very physical style all the way out to the perimeter. There is probably more hacking, grabbing, holding, and "in your jock strap" defenses in the Valley than in most other leagues. That forces the officials to decide what's incidental contact, what's contact that doesn't affect the play, etc. The more decisions the officials have to make, the more they're going to make the wrong decision. Someone might get mugged on a drive and there's a no call. But, touch someone's arm when they're trying to catch a pass, and that "ticky-tack" contact that's so minor compared to something uncalled is more obvious and gets called.
From what I've seen there's an NCAA emphasis on block/charge and the circle under the basket is intended to discourage collisions near the basket. Charge calls are way up in every game in any conference this year.