On the plus side, the weapons are far less overpowered this time around, and the modified Quake engine allows for far more complex level design, on top of a 3D look that hasn't aged perfectly, but still is more pleasing to the eye than enemies that look like they're made from cardboard. They also played it up as much more of an RPG this time around, giving each class a set of visible stats that automatically level up when you've gained enough experience points from killing enemies, giving you an incentive to fight rather than just run past everything. The puzzles are also largely improved, most having solutions that don't require you to activate some unknown wall or something. No, this game will tell you, and you'll probably be able to figure it out without a guide.
On the negative side, the Quake engine. While it's good to look at and everything, you'll have to do a bit of tweaking to get the resolution accurate, set mouse controls, and all that stuff, and it all has to be done manually. It's not a huge complaint, but it's just a quick pain that you have to go through whenever you install the game.
Even if you weren't a fan of the previous games, I'd suggest giving this one a go.