Games whose reputations have improved over the years

Earthbound went from lackluster sales and lukewarm initial reviews to a cult classic to generally being recognized as a masterpiece.

Okami and Shadow of the Colossus both went from relatively obscure to widely regarded as classics and almost obligatory on best games ever lists

Yeah Majora's Mask is a good one

Apparently Morrowind was regarded as the game that dumbed down Elder Scrolls for consoles when it first came out but now tends to be considered the best game in the series.

I remember New Vegas being considered a disappointment compared to Fallout 3 and getting a worse Metacritic score but now everyone seems to think it's much better out of the two.