HL3 needs smarter humanoid enemies that do more than just shoot at me, take cover and occasionally try to flank me or flush me out with grenades. In fact, something analogous to the Assassin from HL1 needs to make a return but which applies more clever tactics to try to get me.
An improved version of the animation techniques used for the zombies in the L4D games. The animation for the combine soldiers in HL2 was good enough for 2004, but technology has moved on and if HL3 pretends to compete directly with the latest in gaming, they at least need to have the combine soldiers to move around as realistically as the L4D zombies, including the way they react to being hit.
Bigger puzzles that may take a whole level to complete, interspersed with combat sequences.
Keep the game progression linear but make the levels a bit more open and with more paths to take.
Related to the idea above, add stealth elements. Take some cues from Deus Ex and add ways for players to be able sneak around enemies in certain levels. If you can sneak on an enemy from behind, a whack from the crowbar should be a one hit kill.