Actually, I'm surprised you didn't list this as one of your beefs, because this is one thing about HL2 that always bugged me.
Why did they reuse sounds?
With the large majority of HL2's sounds being high quality, every now and then you hear someone type on a keypad, or walk across some metal rafters, and then you get the reused HL1 sound effect that sounds horribly out of place.
Granted, I got used to it after awhile, but for all the pros of Half-Life 2, this one should have been an area to see more effort, especially with the amazing sound mixing of the game.