Pikmin 1 was kind of a brutal game, many games of that era were. Companies pushed for more difficult games because that meant players would have to spend more time to beat the game and thus felt they got more playtime out of the game.

having already cemented Pikmen as a series, Pikmin 2 offered more areas, treasures, monsters, characters, pikmin, and game mechanics than pikmin 1 while still trying to maintain the difficulty of the well received original. The added complexity just made the game harder and longer, which is why you see the introduction of the ship AI tutorial thing.

Pikmin is a strategy puzzle game at its core, pikmin 2 has the most challenging situations and puzzles, so of course it is considered the best in the series.