It's all based on preference. Generally, if you have both consoles, you'd just go for the one with more features. If you're interested in online high score competition, then get the Xbox version. If not, either one is game.
Take note, it seems Metal slug 4 music never got a stereo recording, in game form. It sounds as good as ever, but no better than it was on the Neo. Metal Slug 5, however, still has Studio Aqua music but recorded in full stereo. Talk about a tough to rate higher package. I mean, Metal Slug 5 has a kickin' Metal-induced Soundtrack that really does sound great in stereo, but I have absolutely fallen in love with the musical arrangements in 4, even if they aren't in stereo. I mean, MS4 is pure Studio Aqua work in a vein that's just recognizable to those getting Studio Aqua soundtracks. It just sounds like the guys behind the masterful ROTD and Matrimelee soundtracks got their hands on Metal Slug. In MS5, there's more of a heavy metal sound to it(with the addition of more clever sound-effects thrown into the BGM), which is good, but a little further away from the typical Studio Aqua sound. I'll have to admit, MS5 sounds more like a typical Metal Slug, in comparison, and there's more songs given the soundtrack changes mid-level. MS4, however, is truly the big musical departure.
BTW, the Gamestops got it, but EB is a day later than Gamestop, at getting the game.