I think my favourite change so far is the part where they made 'On A Rail' about a third as long and one tenth as complicated. Damn that chapter bugged the crap out of me in the original game!
Something else that's been bothering me; it might just be that I'm playing on "Normal" difficulty, but I'm finding the weapons a bit underpowered. It's most noticeable with the SMG as it appears to take a whole magazine just to take down one squaddie. Maybe my being more familiar with HL2 is skewing my perception, but it's a bit much when I can unload both barrels of the shotgun into a zombie's headcrab at point blank range and it's still coming!