I guess the question I'd ask of those who think mid-major teams are being ranked too low in the PR report, is on what objective criteria should they be ranked higher? If their SOS is bad, and they don't have many Top 50/Top 100 wins, then what logic would you advocate being used to objectively rank them higher (if you think they should be)?
I agree that it is now tougher to get a mid-major an at-large bid. I have experienced that first-hand with my Marquette team. By the same token, though, it is also tougher for a borderline (talent-wise) BCS team to get an at-large bid... if you know you'll struggle to get to 6 or 7 conference wins, the OOC schedule is a challenge to set up perfectly in that situation as well.
But under the old system it was far too easy for a team that didn't have NT talent to schedule 10 away OOC games aginst sims and end up with a Top 40 RPI and make the NT, without having beaten a single Top 100 team. The old system also ridiculously overseeded teams from weak conferences that racked up a huge number of wins.
So both systems had their flaws or downsides. Personally, I like the new system better both because it's more realistic and rewards quality wins, as opposed to simple win total or a deceptively good SOS or RPI. As others have suggested (and I'm not saying it's easy), the way to compete at the mid-major level is to avoid the ghost conferences, and get a bunch of humans together in one league. Then you'll have an opportunity to get several quality wins in-conference, and the OOC schedule doesn't have to be as "perfect".
Also, keep in mind that the game is probably designed from the perspective of a majority of teams being human-coached . I don't think you can design the game assuming most conferences are ghost conferences, and then figure out a way to make things easier for the one or two humans in such a conference. If you do that, you'll have unintended consequences down the road, when/if you do get a lot of humans in a league.