MS3 has the highest replay value: long missions with multiple routes. If you can find a complete first run MS3 kit with the mini marquee, I wouldn't pass it up or wait on it, it is very difficult to find the original mini marquee for it. I made an offer of $200 and paid it to get a mint/complete US kit/first run, I have no idea what it is actually worth tho. I am very happy with my purchase too, this is one game you wont regret buying. Newer MS3 kits usually come with the large marquee.
Although both kits are hard to find, Metal Slug 1 loose carts are a lot more common and it's not all that hard to find kits if you dont mind not having matching serials.