In skyrim I can see why they don't do it. There's spells and some actions that will cause enemies to run in fear, some of which have been featured in previous elder scrolls games, and thus someone would probably b**** about it if they were removed/made practically useless. I approve of them because fear is a badass spell, it makes me feel like the scarecrow, and turning into a werewolf, seeing some knight in shining armour shout "die, beast!" and then roaring at him and seeing him piss his pants is f***ing hilarious.
Also, skyrim's main religious beliefs are similiar to viking beliefs, in that they believe dying in battle will lead to a glorious afterlife. It kinda makes sense, then, that a lot of enemies wouldn't run.
Still, there is something to be said for enemies reacting with fear to you. Especially in stealth games, I find. Picking off enemies one by one, them knowing that you're there, but not knowing where you are. The batman arkham games do this pretty well, with your detective view actively telling you how scared the enemy is.