M249, M40 and Desert Eagle would make sense, considering they're relatively common weapons. Logically, that is. Ingame, they'd just make their HL counterparts useless. (crossbow + 357) Displacer + the alien weapons wouldn't, considering they're prototypes + Shephard went through the prototype labs they were in, not Calhoun or Freeman.
actually my only plans are to include the Shock Trooper, Pit Drone, and Shock Roach.

Maybe voltigore.
Wouldn't want an unbalanced arsenal that ruins what made HL fun in the first place, right?
And believe me, I want to retain that classic HL feel. I've probably played through vanilla HL 20 times since getting it as a Christmas present last year. The expansions not as much. OpFor always crashes on me, and BS needs major improvements. Decay, well... I liked it, but I would have enjoyed it more if I could've quicksaved and had another player.