Half-life always had that sort of "makes sense" kind of design theory where the weapons you obtain are in logical places, like security cabinets or off dead security guards/soldiers.
I'm glad they've retained some of that, but I have to agree with grazr - I was trying to pick up the pistol from dead security guards for a lot of the first level. The flare/throw thing is interesting, but it delivers a different pace than the original game.
I haven't finished it, but so far Black Mesa has been real top notch otherwise. The level design is really at (and, in my opinion, sometimes superior) Valve's ability. The manipulation of the game space to make the Black Mesa complex not just a string of orthogonal rooms, but a methodically designed structure that serves a function, is pivotal in the mod's ability to tell Half-Life's story. Really gorgeous work.