Some of the replacements for the old SFX (e.g. the bleepy bloopy error sound that the retinal scanners and some buttons had, the siren at the start of 'Unforseen Consequences' and at the rocket launch, the houndeye attack cry, the metal clanging sounds, etc) take away the Half-Life atmosphere for me, some of the new textures seem a bit too different to the originals (especially in the office complex and the old parts of the complex that used the 'fifties' texture set, which had a retro feel that hasn't really been retained), some of the weapons don't entirely faithful (not necessarily a bad thing, as they're very good regardless), there are a few physics and enemy AI glitches, some of the transitions between animations on friendly NPCs are a bit abrupt (especially when they die), and some of the voice acting is a bit off and/or doesn't fit the physical appearance of the characters (though 99% of the voice acting itself is brilliant); I'm sure that some of the imperfections will be patched out in the near-future or whenever they get around to releasing Xen, anyway.
I like some of the changes they've made to some of the puzzles to take advantage of the physics, and the fact that they've trimmed and tweaked some of the most annoying parts of the game to actually make them enjoyable while still remaining faithful.
Overall, it's quality work. I'd happily pay money for it.