X > 3 > 2 > 1 > 4 > ANYTHING > 5
My issue with the 1st Metal Slug is the short hop jump and that fact that just about every boss except the last is just spam bombs until it's dead, a common strategy in the series but the 1st suffers the most from this, you can tell they tweaked boss health a bit more in later games to prevent near instant KO's that occurred in the first. Fun game, but a bit too easy.
2's only downfall is the lag, but in my opinion I feel like X improved on it in every way.
X is just so fucking good, perfect balance of difficulty, length and pacing. I feel like a lot of the enemy spawns they added are pretty intuitive compared to 2 and the Slug placement changes are fun. Adding the aliens during the down slope on stage 4 makes that stage a lot more exciting and chaotic.
3 is an amazing game. A lot of people complain about the bullet sponging but I think it's perfect in that regard, only complaint about the game is 3 SHMUP sections in a row and the 3rd one drags on and seems unnecessary, pacing would have been perfect with just the side scrolling and space SHMUP portions, the one inside the alien mother ship was just overkill. Also the 4th stage boss can go suck a dick with the gold lasers
4 Is alright but nothing special, it reuses a lot of the older assets of the previous Slug's but I still find the game enjoyable (as long as you don't take the mummy path, that section is just horrible and lazy) although not great but certainly not bad, the soundtrack is really good.
5 Is absolute shit, they added a slide mechanic but it just never feels useful, the stage design is total garbage and the boss fights aren't fun, the last boss is a joke. The game was unfinished and it shows. Some of the audio tracks are cool and that's about the only nice thing I can say about the game.