Since the category is Underestimated not Underrated...
Baldur's Gate was released with some obscurity. The big game that year was (1998) supposed to be Ultima 9 and there was buzz with Fallout 2 as Fallout 1 gave it a lot of word of mouth. Dungeons and Dragons as a name had been faltering for a few years.
Coincidentally, Icewind Dale was supposed to tank in light that it had the same release date as as Diablo 2.
Diablo 1 had a poor initial release as its satanic box art put a lot of people off. But that's not an RPG of course.
I don't think anyone realized the Gold Box games would be as big as they became, although Ultima was still outselling it.
FF was a boulder that started downhill in Japan and is still rolling.
Ultima Online took EA completely by surprise with 55 000 accounts in the first month. It overwhelmed their capacity.
EQ's smooth 3d graphics unseated UO.
Warcraft, although had tremendous hype and expectation, I doubt anyone would have believed that EQ would suffer such losses.
City if Heroes was a minor hit, defying the pattern fantasy RPG's.
Wizardry I. No one thought such a game was possible with the technology available.
Ultima 3 ditto.
Ultima 4 the one CRPG that made a complete Gestalt Shift in gaming in general. Later games would simplify the morality feature to a simple Karma meter.
Ultima Underworld: the first major smooth scrolling FPS. It didn't do well in sales, yet keeping the Ultima tradition it radically changed gaming forever.
King's Bounty: few people played this game but it launched the Heroes of Might and Magic series
Might and Magic 6 revived the traditional CRPG which was thought long dead. I contend it was inspired by the emulation craze of the mid to late nineties. 3do realized such games were marketable again.
Gemstone: AOL's MUDD coughed up $2 and hour from anyone that played. Such games were so successful they scrapped the original NWN when no one would leave when they went unlimited monthly.
Colossal Caverns Adventure took over many a mainframe and was launched at roughly the same time as D&D PnP