The UK never even got MM6, hell not sure if we got 5. Not a fan of either though, everything after 2 was just a downhill journey until the awesome MM9 came out.
Not sure if it counts as underrated or simply obscure but Mother 3 (aka the next Earthbound) was a fantastic GBA game and it's Japan only release is a sin. It's also a huge shame that Ganbare Goemon 2 (the second Mystical Ninja on the SNES) was Japan only as it's amazingly good (unlike the first one) and after the first one came out on the Wii's VC I did have my fingers crossed for it.
Talking about Mystical Ninja sequels the second N64 has to be one of the most underrated games of all time, seriously it's just crazy how much love that game doesn't get.
Oh and Contra 4. It was such a fantastic revival, and then Konami do Contra Rebirth as if Contra 4 didn't revive the series, not to mention that it STILL isn't out in the UK. Contra 4 is by far my favourite Contra game, even knocking the first one of the pedestal it's been on in my heart for so long.