Just finished Witcher 2EE, after playing WitcherEE. For me, Witcher 2 is better in every aspect, particularly the branching story, highly meaningful choices that deeply impact the entire world and aren't rolled back in the end (siding with Yaevinn all the way effectively preserves the status quo, as any concessions to non-humans are quickly taken back by Foltest), better reactivity in combat, a more focused, fluid gameplay... But really, it's the choices and lack of an "optimal" path that make it better. In Roche's path you ultimately choose between an united Temeria and massive witch hunts or prospering magic practitioners but a fractured, broken domain that used to be Foltest's.
One big flaw in WitcherEE will only be understood by people who read the entire saga, from Last Wish to Lady of the Lake. WitcherEE is highly derivative, borrowing plots, quotes, characters from Sapkowski's work en masse. It's understandable as an introduction to the universe, but the amount of copy/pasting done is jarring to anyone who read the original series. It's as if the developers held back, afraid to step outside Sapkowski's work. With Witcher 2 they're much more confident and take it in new, bold directions.
Witcher 2 <3