@moturimi1 -- what don't you like about the flute? That was one of the instruments they were pretty proud of after their tweaks. If I have one criticism of the flute, it's that the vibrato is slightly too fast, but otherwise, it's a huge improvement.
I agree with you on the trumpets (or whatever horn instrument that is) in Dark Forces. Particular in the 3-10 second period of the song, and again in the 18-21 second period. Interestingly, the horn instrument in Tie Fighter sounds great. That's why I think it may two different horn instruments.
In Descent 2, the one bass instrument that plays the main melody sounds overly distorted, like a blown speaker cone.
In general, I think the electric guitar is a little too distorted, but that could just be my personal taste. In some songs (like Duke Nukem) it sounds fine, while in other songs (System Shock Medical at 44 seconds in) it sounds overdone. So I could generalize that if you have one electric guitar instrument that will be playing both rock songs as well as synthy or softer tunes, the guitar distortion should be tune back to accomodate the softer/synthy tunes.
Those comments are all based on Phil's video linked above.