The inverted-gravity effect in The First Encounter and The Second Encounter has been removed and Scythian Witch-Harpies can no longer carry Beheaded Kamikazes due to issues regarding the engine. Not everything has been kept in the remakes.
Gameplay-wise, Serious Sam HD functions pretty much the same as it does in the old games. The level layouts have been kept, but nearly all of the graphics, textures, models, lighting and special effects have all been updated. Serious Sam HD consists of high-definition remakes of Serious Sam: The First Encounter and Serious Sam: The Second Encounter using a newer version of the Serious Engine: Serious Engine 3.