Please, don't let GK3's disguise puzzle deter you from completing the game! It's a fantastic, multi-layered game that checks almost all the boxes you are looking for: dark, 3rd person (technically), strong story (arguably the strongest, most well-crafted story of any adventure game ever), (blockily) realistic, and from an appropriate time period. It's in (clumsy but totally workable) 3D but you can't have everything!
Also, that puzzle has been widely acknowledged to be extremely unfair (in fact, it's been cited as, more or less, the death rattle of adventure games as a genre) so you shouldn't feel bad looking up a hint for it in UHS, for example.
EDIT: As far as must-play games on your list go, IMHO those would be BaSS, the GK series (each more amazing than the last, true gems), and Sanitarium. They're also all very much along the lines of what you are looking for. The Monkey Island games (at least the 1st two), while not dark, are definitely also a must-play.
And, please, for all that is holy, do NOT even think about Still Life 2! Never have I played such a buggy, plodding, unimaginative, stupid, plot-hole-riddled, awkwardly-controlled (that inventory!) mess of a game.
P.S. Also you have to play more Fallout, and Fallout 2! You will thank me later!
