Star War Jedi Knight II: Jedi Outcast: Way too many levels before you get your lightsaber in a game engine where the lightsaber combat is the most fun thing you can do. It's possible to play for hours and put it away concluding that it's just a run of the mill shooter, but that would be a big mistake.

Also both Knights of the Old Republic games take a long time to get to the good stuff. KOTOR I has Taris and Dantooine, KOTOR II has Peragus and Telos. It just takes a long time for those games to set up their main conflict, so a lot of the stuff you do on those first planets feels a bit aimless at the time you're doing it and pointless by the time you're done.

Final Fantasy XII is yet another JRPG that has this problem. The very first scene/tutorial level is actually pretty great - you see some politics happen, a betrayal, and it's all in media res while you learn the game's strange but fun combat system. Then you switch to the actual main character Vaan and it takes like six hours for the game to get interesting again.