Metal Gear Solid 3: Subsistence
I wasn't sure about this one for a lot of the time I was playing it. Most of the new gameplay features add depth but detract from the fun, in my opinion. Limited inventory space, having to use camoflage, feed yourself, and mend your wounds and breaks sounds cool and realistic, but it just adds a ton of menu navigation to the normal gameplay experience. I don't think it really enhanced my experience needing to change my uniform when I move from the jungle to the inside of a building or click on a few different items to stop me from bleeding away any more health in a tight spot.
I was also concerned about the story, I was one of many who was fed up by the direction MGS2's story went by the end, but since then I've come to appreciate it more, and MGS3's tale didn't seem as twisty and interesting, perhaps in response to that backlash. MGS3 has more of a focus on character and emotion than political quadruple-crosses, and ends up being the most satisfying and best story in the series, in my opinion. And let's be honest here, thanks to the series' deep but increasingly dated and clumsy gameplay engine, the story is why we play Metal Gear. I don't have to tell you the visuals are amazing, and the sound is quite good too, well acted as always, and with some good music and maybe the best use of a classic theme I've ever seen near the end.
Subsistence also has some great special features, especially the inclusion of the first two games from the MSX (this being the first time MG2 is available legally in the US) and the hilarious Secret Theater.