Sam now has a new model, and no shades. He is a lot less like Duke Nukem, like he was in Serious Sam 1.
Rocketeers, Bombers, Firecrackers and Kamikazes looked more muscular than in Serious Sam 1, and they had less human-like heads (except Kamikazes, who have no heads), without a mouth and with glowing light blue eyes and they all had a belt with a skull on it. Kamikazes' back also looked different.
A "Multikill" system, which multiplies your score if you killed multiple enemies with a single shot. (x1 multiplier for each enemy killed) The more multikills you do in a short period of time, the higher the multiplier.
A Life system, which re-spawns you in place when you die.
Auto-aiming, as aiming with the controller would be harder and uncomfortable for some people compared to aiming with the mouse.
You could allign your favorite weapons to the X and Y button by selecting a weapon and holding X or Y, then press X or Y again to select that weapon.