Learn from the latest Harry Potter game, Bethesda! We the people demand a cover-based shooter! Litter the environment with chest-high walls and to hell with immersion or atmosphere!
I think I should be happy that Mass Effect 2 was my first and only cover-based shooter-RPG. So, it didn't hinder my enjoyment over it.I can understand how people must hate them already.
Learning from other games is good. Redoing mistakes is not.
Daggerfall: Critical Strike, Dodge, Medical, ability to kick in doors, dis/advantages, spells that gain power, seasons
FEAR: kicking in melee combat, seeing your body and shadow
Thief 3: knocking out and backstabbing, again seeing yourself and shadow, moving light sources and soft shadows
Mass Effects and Dragon Age: well written dialogue, NPC that feel more like people than NPCs, choices and consequances.
The Witcher: choices and consequances, gray morals, tasteful advlt content, nasty humour.
Gothic series: design of outdoors, multiple possible ways of doing things/quests
Mount&Blade: realistic horses and mounted combat, visually realistic armour and weapons
Doom 2: Arch-Vile (the demon that can set you on fire when he has visual contact)
URW: multiple damage, armour and wound types. Survival elements such as tracking, hunting, fishing, cooking, first aid, crafting, hunger/ thirst/ exhaustion/ freezing, seasons
Edit:
How do you make daggers and the like useful?
AGI gives damage bonus for small weapons like daggers, while STR gives bonus for big weapons. Damage per time units is what counts, and lighter weapons are swung faster. Also, it would be neat if you could conseal smaller weapons and take them where heavily armed people are not welcome.
Being able to throw your weapon at any time would make spear fighting, as well as having multiple daggers with you, awesome. Daggers could also deliver poisons more effectively into the blood of foes, while stuff like maces and quarterstaves should not be poisoned. Think about it: a small blade goes through armor, doing not much damage put penetrating through and delivering the poison. Bigger weapons would just bash the armor and deliver 'normal' damage.