your issue, mjp, comes down to 1 thing - record vs top X... top 25, 50, 100 (and maybe 75?). for example, your record vs the top 50 is 3-4. that suggests you are worse than the average top 50 team (which would be ~25th, a 6 seed). your record vs the top 25 is also 3-4, which is definitely better, that pegs you around a 4 seed. its your record vs the top 100 that is killing you, 6-5. that suggests you are basically an average (or slightly above average) team for the top 100 group, which puts you around 45-50, 12-13 seed.
its unfortunate you are in SUCH a bad conference. its going to be tough any time you play in a conference with *one* team in the top 100 rpi. how will you build your record vs top 25/50/100? all you've got is non conference. id try to schedule almost all my teams in the top 100, and a bunch in the top 50, but within those constraints, you want the weakest teams you can find, so you will come out with a better record. you have 6 top teams and split them, i think thats good - but the problem is you didnt leave enough games to pad your top 50 and top 100 records. you most likely would have won most of your vs 35-100 rpi games (or maybe not, but then you don't deserve a 4 seed, either), problem is, you don't really have any.
for the record, i think most conferences are workable, but a conference that bad is always going to make things more challenging. thats like, a bottom in the world conference, which is the worst place for top teams to be. even a bottom 3rd-4th type conference is fine, because you get some double digit rpis to help your record vs top X. the new seeding algorithms seble did absolutely favor those who are able to play, and win, those games.