I have a hard time envisioning a "tactical" system that doesn't incorporate the idea of cover, some how. It's kind of a big deal when people are shooting at you.
How it's handled, though, can have a massive effect on gameplay. Xcom opted for a faster, more free-ranging style of turn-based play than a lot of systems because they wanted to appeal to a larger crowd. You could run across large swathes of area with an enemy in plain site without getting shot at, due to the low number of unis around (and their predictable setup, but that's another issue).
Cover is best handled in concert with other topics, such as suppression. Furthermore, I'd discourage there being a straight up percentage chance to hit somebody in decent cover. That always drives me crazy. If they are shooting from an angle, sure, get some chance in there, but hard cover should completely protect from at least one direction, because it increases tactical depth when you absolutely MUST flank an enemy rather than just throwing enough bullets at them that something is sure to get through. It also makes the use of ballistic trajectory weapons (grenades, mortars) more tactically focused than just "I want to hit lots of guys hard."
Finally, overwatch/interrupts are a must have. A guy taking a ton of fire on his position (but safe for the moment due to afore-mentioned hard cover rule) should have a very low chance of survival if he just up and runs. He needs allies to come along and provide covering fire, thereby suppressing the enemy, which gives him a chance to move.
All in all, the newer Xcom was pretty good, but it handled all tactics in a very arcade style, playing fast and loose with some very nuanced issues. It grated on me now and then.