I think the most recent episode, with Mr. Horse as the psychologist, is a vast improvement over the first. No gay jokes, less gross-out humor, and, well, it had Mr. Horse in it.
I recall that John K. said in an interview a while back that he intended Stimpy to be gay, and totally devoted to Ren, while Ren just sort of dealt with it until he could get his hands on a nice human woman.
As for the far-out pilot, I don't know if it was as extreme as it was as an indication of what was to come, or just to show that this wasn't quite the R&S we'd grown accustomed to. Only time will tell, I guess.