Personally, I'm torn between Super Mario RPG and M&L:SS.
But, if I had to choose one, I suppose it would to be the former. While M&L was more fast-paced, hilarious, and finally gave some love to Luigi, I think that SMRPG had a better story and was more extensive. Also, I loved how SMRPG was...
Really? I think that it's still the strongest RPG Mario game in the series. Squaresoft was just able to handle the genre the best, in my opinion (since it's their specialty).
Anyway, I'd have to say that every Mario Party game after Mario Party 3 has deeply disappointed me in some way...