You know what, I'm rewatching all the episodes in chronological order now, for enjoyment but also to identify set photos, but I can't decide on the season! There've always been stronger and weaker episodes in every season in my opinion, but to really arrive at a list of seasons, I would have to score each episode and add up the results. I couldn't think of any other way.
I said S1 was my favourite, but that was mainly for nostalgic reasons and the initial impact the series made.
I agree Dewey as a character (understandably) got more interesting as the series went along, Justin as Reese remained terrific, but Frankie as Malcolm developed an annoying tendency for two-note acting: either complete eyebrows-up bafflement or frowning bafflement-cum-irritation. I find that strange, because Frankie as a kid was one of the most expressive actors his age ever. Even then, he had some really great moments in episodes like "Ida's Boyfriend" and "Pearl Harbor". Jane and Bryan were impeccable throughout.
As for supporting actors who brought in new, interesting storylines, it's a toss-up. The great Cloris Leachman was introduced in S2, but then there was the terrific Daniel von Bargen as Spangler in S1, and the funny Mannkussers from S4.
Rich