Good data.
I think that part of the issue is that some of us have had higher expectations for Maroney than for Morris and believe that we see him piss away opportunities to increase his YPC.
I think that you frame it in an excellent way: Maroney is the best running back on the team (Faulk is a 3rd down back for discussion purposes), but why is there not a wider gulf of separation between him and the other options?
(Disclaimer: First, let me state that I was really pissed off that the team didn't find a way to get Steven Jackson in the draft, so I was not a fan of the Maroney pick. I figured that if Jackson wasn't worth getting in round 1, why the hell should Maroney make the cut? I wanted Ngata, who was already gone, or Kiwanuka. I still don't like that they passed over Jackson but made sure to take Maroney, but I try not to let that affect what my opinion of LoMo.)
Some theories I've looked at:
1.) The zone blocking isn't opening up the sort of cutback holes that a Maroney would use, but any fool can run behind Mankins and Light and get 3+ yards per carry. This puts Maroney at a distinct disadvantage, because the offensive line's frequent failures to open holes prevents LoMo from cutting back, and that makes it seem as if he's dancing when he's actually waiting for a hole to open that's never going to show. Since Morris and Jordan (And Dillon, etc...) don't run with this style, they are not impacted as negatively as LoMo is.
2.) LoMo is a bit of a Nancy and doesn't like repetitive contact.
3.) The team uses LoMo pretty much the same way every time, so teams can focus on that and shut it down.
4.) LoMo sucks.
5.) LoMo can't play hurt (I'm talking hurt, not injured).
6.) LoMo tries playing through injuries when he shouldn't.
7.) McDaniels can't, or won't, run the running game in a manner that suits Maroney's strengths. For example, why the hell isn't Maroney getting some fakes, slipping through the line and making catches just past the LOS? That would make the defenders hesitate and would make life easier for LoMo. Also, why no sweeps, or quick swing passses? Why no direct snaps? Why no Wildcat formations, etc.?
Personally, I tend to lean more towards #1,#3, and #7, but I'm open to pretty much any of the above (except #4, which I think last year showed to be untrue) if further information comes forth to change my current position that it's mostly the combination of poor blocking and pigeonholed playcalling.