Deus Ex does come to mind here. Larger urban enviroments with bigger populations, SERIOUSLY improved voice acting in regards to the non-american characters, improved graphics etc.
The game had a really good story and evoked some seriously interesting philosophical ideas, and that is a very good ground to build a fantastic game on.
Call of Cthulhu: Dark Corners of the Earth also comes to mind, but mostly for graphical reasons. While I am perfectly happy with the graphics as they certainly get the job done, I would have loved to see the horrifying imagery of cosmic sea monsters and Lovecraftian settings with graphics on par with bioshock or something similar (especially the water animations).
Another reason for it would be to put games of Lovecraftian themes on the map, and perhaps make the game developers more interested in making more games out of H.P Lovecrafts works, because Call of Cthulhu: Dark Corners of the Earth was certainly a top notch game in it's own and a top-notch adaption of the original source material.