To make unique loot interesting, I'd say take a look at ToME and how DarkGod does it. Really great. Are unique items better than non-unique? Eh, its debatable. Unique items usually confer very SPECIFIC bonuses, and thats about it. Whoa I found an AmmoBox of Doom and it gives +200% ammo and.....its only for pistols? WTF? Situational. My pistols usually only get used for those batteries that fit into any slot.
Also there are "rare" and "randarts" in ToME that balance out the mix nicely as well, they again come with nice bonuses, usually pretty interesting, but a lot of the time its not what I am looking for in my current situation. Plenty of times will I junk a unique or randart or rare in ToME because it dosent fit by build and / or playstyle.
Uniques dont have to be "+5000% damage!" and become the obvious choice, they can be "Your Assault Bots grenade launcher now shoots Smoke Grenades! Who dosent love Smoke? It blocks Line of Sight to save your butt. Well, if you're the type of person who likes to do damage you probably don't like it. Smoke isnt exactly known for its prowess in inflicting damage": Grenades now make smoke, -80% damage.
See? How "obvious" is that? Its purely a panic button. Cant shoot what you cant see, and you arent doing damage. But if you are in trouble it will make a quick escape, OR maybe there's that pretty nasty DoomBot pack on one side of the room you don't want to deal with yet, so you smoke them and clear the rest of the room first. Tactical choices galore!
"Spider Bots! You've manufactured some pretty specific servos, gryros, gears, and other pieces of techosorcery and, well, your turrets have legs now! Unfortunately in order to make this even slightly effective you had to strip a lot of weight to get it to not collapse on itself, and shielding and firepower to power the legs movment.": Turrets can move. Turrets have -50% shields, -35% ammo, -40% damage.
Again not very obvious as "better". My turrets can move, oh joy, too bad I've gimped their offensive output. But maybe they're good for scouting / taking a few shots, or just being a minor source of additional damage instead of the towers of death they currently are.
Alternate power source: "Stealth drains at twice the rate, but will add one round to a random Energy weapons current ammo"
Remarkably, Stealth isnt just for using Virus and opening doors. Now it can replenish your precious ammo stores. Suddenly Stealth becomes a lot more interesting because now you have more choices. Do I burn it for power, or do I keep it for survivability?
Or even less specific: "+50% weapon damage, -40% weapon ammo due to increased ammo size"
"Unique" dosent have to mean "omgwtfzorz I kill everything in 1shot uber, lawl nubz aint got no 1337 lootz gon die"