My profile should say it, but to save you time, I'll say that I dont really have a favorite Zelda game, due solely to the fact that the series has too many games and have gone for so long by the same general formula that's shown to still be pretty successful to this day. As far as refinement goes, TP, though the least innovative, is from a technical point of view, the most refined, polished, and presentationally powerful Zelda to date with the most expressive characters and one of the more heavily executed plots. From an innovative point of view, OOT brought the series into 3D, but that would've been done eventually anyway--not to say it's a fact to be overlooked just for the sake of that, but the real fact is that it's more of an evolutionary step than anything else. I'd have to say MM is probably the most unique LoZ amongst at least the 3D Zeldas; the only other major game to have anywhere as close a focus on the supporting cast after it was TP, and that game involved the supporting cast in the main plot more than for the sake of sidequests to benefit the main plot as was the case with MM. PH probably had some of my favorite characterization with the likes of Linebeck and how they dealt with him as a semi-sidekick and the relation between he and Link was a good one IMO.

While I don't have a favorite, I try to see what the most major ones have the best of. ALTTP for example, was the first to truly delve into the plot of the series, LA was the first to give Link a truly deep connection to a character in the supporting cast, and WW was the first to have Link become a much more expressive, personable character, which was emphasized even further in TP (hence why TP Link is probably my favorite Link). From a plot-based point of view, these qualities among others are what made the games unique in their own rights.