The reason for the general abscence of boss fights in games probably has to do with the glut of shooters and open-world games in the market right now, and neither genre is particularly fit for making good boss fights (shooters not at all, open-world games tend to have level-scaling).
Boss encounters are better fit for games from the action-adventure, hack-&-slash, and RPG genres. The first one is regrettably much rarer in the modern era than previous generations, the second has seen a dip in popularity, and the third has moved heavily towards more open-world games. Still, there are games which great boss fights out there.
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Xenoblade Chronicles is one I've been enjoying a lot recently, and is something of a throwback to earlier RPGs (with some modern improvements); the sort of game which made people fall in love with the Final Fantasy franchise. The only real downside is the graphics aren't that great, but the art design compensates for it. But yes, we want boss fights to be the focus here. XBC has some very good ones, and the difficulty is perfectly tuned for most of them. The combat system also places a great deal of emphasis on the party's morale (called "tension" for some wierd reason, must be a translation error), and in the case of boss battles this becomes a very interesting element. When an ally falls in battle, you can revive them by walking up to them and physically getting them up (and you can often follow up by encouraging them); however, them falling means the party's morale just took a huge hit and you're in recovery mode for a bit (a chain attack can really help here). Bosses are naturally longer fights than normal, so allies falling against the tougher ones can be expected; this gives many boss fights a bit of an ebb and flow to them, and the gameplay elements often add an emotional rush when you claw out from the grasp of defeat and beat your foes.
Dark Souls is another recent game with great boss fights, though it is handled quite differently; they're hard as hell, and simply beating many of them is a feat by itself. They have their quirks and tells, and you'll die many times learning them and how to take advantage of their missteps. However, it's a very frustrating game to play as well; you will screw up, you will die, and your performance can easily enter a downward spiral as you just screw up more and die more due to the increasing frustration. This is offset by the huge burst of satisfaction when you finally conquer something, but there will be times you'll have to step back for your sanity.
Sadly, both games are something of niche entertainment right now; the mainstream is focused on games and genres which don't take to good boss fights very well, so they're just harder to find as a result.
