Metal Slug 3 is a masterpiece, a fantastic game. However, Metal Slug X is also an incredible game, and definitely worth picking up. Personally, I love the entire MS series, they're all great games in their own right and worth getting.
But you have to weigh the costs in every case. MS3 for $400+, or KOF 2000 for $332, or several of the coming flood of carts at very reasonable prices . . . its your choice.
Its a shame they didn't have a very high production quantity of MS3 carts . . . they filled preorders and that was it. Stupid philosophy, I think, but I guess they got burned by overproduction of many carts in the past and just decided to keep production to a bare minimum in the future . . .