Hmmm...
I flew them literally on their 1st day of operation and several times since.
I've never had a problem getting mileage credit. In fact, I think they post much quicker than the Legacy airlines do.
I can't relate to your issues ref bad seating on last minute (high fare) purchases as my travel patterns usually allow me the benefit of advance purchase fares.
As a long standing CO Elite, I admit it's strange being hit with a checked baggage fee and being the 3rd or 4th group to board
However, I've assumed that the higher fares booked into Main Cabin Select (no bag fee, more leg room, free food/drink). Unless of course you are so "last minute" that you're buying within 24 hours of the flight so MCS may have filled up with people buying upgrades. As a generic rule of thumb, I bet most folks flying once or twice a year are not willing to pay for the upgrade (or if they even know about it).
As they grow, and get more of a base of very frequent flyers, then things may change. One of the main complaints I see on this old thread are ref points expiring after 18 months (even with recent activity). That has since been rescinded. So yes, as a relatively new airline, they will be tweaking their product to find the right balance between "being innovative" vs "remaining competitive". But IMHO, I can't agree to your comment that they're acting like "oh poor us, we're still learning to be an airline".
Steve