I have never really liked "initiative," in the trad RPG sense, in
any system that has used it. Whether it's rolling dice or drawing cards, it tends to come down to this random fiddly thing that grinds the excitement and drama of "shots fired!" to a standstill, and then is set in stone for the rest of the battle. That's not what "initiative" is. The Reflex system was a noble attempt, especially within this genre, but it's pretty overly complex and annoying to track when it comes down to it.
Coriolis does this thing you're talking about, btw. If you take the bonus, you are obligated to use that weapon on your turn. Somehow this makes shooting with a compact pistol a "faster" thing to do than just sprinting flat-out with no weapon at all.
Anyway, maybe this is a digression, but I prefer systems and hacks that either do simultaneous or narrative driven actions, or a simple binary system. One such system for T2K could be: start of combat, roll your CUF. If you succeed, you'll act before the enemy. Otherwise, you act after. You could have particularly elite or dangerous NPCs roll as well, or use modifiers to reflect that, account for surprise, etc. This would feel much cleaner to me and reflect at least a small degree of actual character and situation.
Last, I'll just leave this here:
a really nice write-up of a clean hack for a similar problem in Mothership. I agree 100% with all of his "whys" and almost all of them apply to T2K as well.