Here is the deal, as unbiased as you can get. The general consensus, as far as the population outside this board is concerned, is that 3 is the best game. However, X is the only slug game that was on IGNs top 100 games of all time list, although it has now been removed. There is a lot of love though for the first Metal Slug as well.
So all that said, overall the best are considered to be X, 3, and 1 (not in any particular order or rank)
All this crap about Slug 2>X is just a fad existing only among a dozen people on this board. It's the same thing that happens to people who listen to one band all the time. After they burn the singles or more popular songs out, they go to the B sides or non singles. And then it becomes trendy among fans of that band to regard the B-sides as more "artistic" than the others because it's underground, not as well known or liked, etc. The truth of it is, just like MJs "Thriller" album doesn't continue to sell because of songs like "Human Nature", the Metal Slug series isn't a popular and highly regarded game series because of Slug 2. Remember that when deciding which slug to buy next.