For example, compare the Diablo games. Diablo 1 and 2 had fantastic soundtracks that really encapsulated the mood the game was trying to create. When you were in Hell, the music was evil and ominous. When you were in Tristram (the main/only town, for those who have never played), the music was melancholy, bleak, and dark; you could almost hear the wolves howling in the distance, and there was a palpable feeling of doom over the town. Hell, I often found myself standing about in town just to listen to it over and over again. Diablo 2 was, in many ways, even better, since it captured a wider variety of moods; the rolling percussion and the mellow flutes accompanying your desert explorations; the ominous bass, creepy skittering sounds, and sparse guitars as you delved into a crypt crawling with the undead; the music pulled you into the environments perfectly. Then, there is Diablo 3. While I love the game on most other fronts, the music really took a dip in quality. The first act of the game does have some decent atmosphere, but nothing really all that special. The sound effects are spot-on, but the ambient music rarely adds to mood, and I prefer to put on my own music instead.
Often times, the sound portion of atmosphere gets sorely neglected. With the exception of horror games, which rely heavily on atmosphere to draw players in, many games really can be muted without affecting gameplay (except for when people talk). They use little to no ambient sound, and while for some games this makes sense, because there are some cases when the sounds of the world itself coupled with a few understated tracks here and there are enough to do the job (some games, like Silent Hill: Downpour and Dishonored, utilise minimalism quite well), but many miss that chance to immerse players more fully.
There was a time when most games had an amazing soundtrack, one that telegraphed the mood and feel of each level, to the point that many actually stand alone (I personally own many, including that of Chrono Trigger, Super Metroid, and Diablo 1 & 2), and some companies keep this alive, like Nintendo, Bethesda, and Arkane, but many don't seem to put in the effort, and it shows. Games have better graphics then ever, are telling better stories in better ways, and are playing as well as or better than ever, so is it too much to ask that the sound design might be that great as well?