Answer:
Without a doubt, Pikmin 2 is better.
The original Pikmin involves you hunting for 30 pieces of your ship within a limit of 30 days. Thus, you have a time limit which makes the game more stressful than usual. If you like a challenge by getting items before time is up, then this game is for you. However, because you only have 30 days, the game will not last that long.
Pikmin 2, however, involves you searching for treasure (and even dead bodies of creatures you defeat) in order to pay back the 10,000 Pokos that led the company of Hocotate Freight into debt. Once your debt is paid you can get all of the treasures, and after that you can still raise Pikmin. You have unlimited days to complete all of the tasks, which means some days can be spent just getting more Pikmin while others may involve completing two caves. Not only is there a challenge mode, but there is also a two-player mode to go along with the great adventure mode. Most people select Pikmin 2 as the clearly better game, simply because it adds a two-player mode, a challenge mode, and a very intense and thorough story mode that you can accomplish at your own leisure.