SQ6 is my least favourite of the series too. Although it is funny in parts, the general feeling that I get it that it is trying to be more grown up and better produced and is trying to be consciously funny. The constant putting Roger down starts to grate for me too. Yes, Roger is a bit of a doofus but in previous installments that is a sideline to the main story instead of the central theme. And in the first few games, he is trying to save the universe and the comedy is almost coincidental whereas SQ6 tries very hard to be funny all the time.
I can see how other people would see it differently though, particularly if SQ6 was one of the first ones that they played instead of playing the earlier ones first. SQ5 was on the way to becoming a bit like SQ6 too, but I didn't mind that so much because the visual style was very much like SQ4 which I liked. My favourite is probably SQ3.