On your issue No. 1, I'm not really seeing that as a problem, especially since we don't know additional information like SOS, where the conf. ranks in RPI, etc.. An RPI of 45 is not a lock for the real-world NCAA unless it comes from a power conference. There's plenty of recent examples of RPI teams in the 30s and 40s being bypassed due to SOS concerns and/or record vs. Top 50 (and below 150) RPI schools. Conference tournament champs from lower-tier conf's always eat bracket slots that, if you seeded straight off the RPI, they shouldn't have.
Does it suck when you think you should be dancing and instead find yourself NIT-picked...heck yeah, but that's the reality and beauty of the post-season (both real and WIS). Don't like it? Don't leave it in the hands of the selection committee.