The crate puzzles and stealth (yes, I know it's been said) were incredibly irritating, the first because often implementing the solution took a great deal longer than actually coming up with it and the second because it seemed so unrefined, unrealistic and sometimes arbitrary.
Spoiler:I'm in a prior or whatever's office but the only bible in the vicinity is in the pulpit... so I have to sneak past two armed guards again... twice?
The writing was also a bit hit and miss (though the Irish TV presenter is one of my favourite characters from the whole series, and I detest the Irish) and the character design inconsistent (Bruno in particular was perfect but George and Nico felt completely wrong.) The part where:
Spoiler:George finds King Arthur and Excalibur, Nico appears to die, then in a surprise twist doesn't and George beats up a dragon
was particularly dire.
Overall it was still a decent game, with a good visual style in general, some worthwhile puzzles and gameplay experiments (the Quicktime events had potential, though they weren't always implemented very well) and sometimes excellent writing. I'd rank it below BS2 in charm but higher objectively.