Pikmin 2 was inferior because it lacked a time limit. Now, this is coming from somebody who absolutely detests time limits in almost every situation, but the 30 day limit really made the first Pikmin special. Every time I let a pikmin die in the first game my heart broke a little, so I would fight my hardest to keep every little critter alive. In Pikmin 2 they all seemed too expendable since I could just dedicate a few days to harvesting and then go back to the actual game. The balance between completing goals and getting more Pikmin was lost.
Both games are fantastic though. The first Pikmin is easily one of the greatest games on the Gamecube, and the second most charming piece of software I have ever seen (first place: Animal Crossing)