These are my only 2 issues also, stepping over the rocker panel to get in aggravates me every time I get in/out, and it's one of those things you never would notice until you have to do it. Other than that everything else is a known "jeep thing" IMO. If ya don't like certain doors the good news is there's more alternatives out there than any other vehicle offers. I personally love my half doors for summer time, I don't think I'll even buy uppers for them, then in fall and spring I'll switch back to the full doors. Granted my opinion is based on all the mall crawling I do so I don't have the credentials to participate in the trail door debate.
I will say that for all the full door love this thread has gotten, I can't believe there's not more mention of the fact that there's no where to rest your arm and it makes it uncomfortable and awkward to drive for me.