For me it's Diablo II. Granted I've played my fair share of D2 since launch, and also recently on a private server with a comrade from hexbear, but I still feel like years later the game didn't grab me as much as D1 did.
Granted I don't hate D2, but for a game that I keep coming back to, D1 takes the prize.
Granted, I haven't played it myself yet, but Mega Man Star Force 2 is that for a lot of fans of that series. The first game already got a lukewarm reception because of how it was simultaneously "just more Battle Network" and "not simply more Battle Network", but it has a very heartfelt story and some people are turning around on it when they can judge it on its own merits instead of constant comparisons to Battle Network, which has better gameplay. It still sold a decent number of copies.
The second game basically killed whatever momentum the series had by then. The story got dumbed down significantly which made it feel even more like Battle Network (although it still has its moments), the space theme was lost to "lost civilisations" shenanigans that many fans weren't interested in, the gameplay changes were meh and you frequently had to navigate through a maze-like "Sky Wave" with a too high encounter rate. Sales numbers were well below expectations.
The third game has the best gameplay by far and a story close to or as good as the first game, but the damage was already done. It sold the least of the three games. But at least the series ended on a high note with very few loose ends.