Been thinking about this and among the games I play I find it to be exceedingly rare for the original to be the best in the series.

To be fair, there's a lot of games where I simply never played/experienced the original, even if I'm fairly confindent they wouldn't end up topping their successors; Warcraft 3, Starcraft 2, Diablo 2, SMT 3: Nocturne, Persona 3, Touhou 7, Dynasty Warriors 4, Civilization 4, Metal Gear Solid 3, Zone of the Enders 2, NieR:Automata, .hack://G.U., and even Final Fantasy X all fall under that.

Meanwhile some other series where I did play the originals and sequels that surpass them: Crash Bandicoot 2, Tekken 4, Valkyria Chronicles 4, Ys VIII, Trails of Cold Steel 2, Umineko When They Cry, Super Mario World, The Great Ace Attorney 2, Danganronpa V3, Zero Escape: Zero Time Dilemma.

I guess if you squint, Fate/Stay Night is the best in the Fate franchise although it's mostly a franchise of spin-offs rather than sequels. Really this question has made me realize just how rare it is I follow a series through entirely if I jump late on what is generally considered to be their better games.