Except that, with the mission generator already stuffed with a huge amount of stuff, locking a tech (even a not very important one) behind a single mission and/or capture seems a bit counterproductive. I assume the reason behind VIP kidnapping and Saya reward is to make the research largely independent from missions, since they are too random. If anything, the reward could be items that are rare/lategame tech - nuclear lasers, defender armor, Python HSR etc. for the easy-medium missions, with Impalers, Gattling Lascannon Parts, gems and perhaps even an Orb for the most difficult ones. That way you have some reward (that works for a time), but without upsetting the general tech balance. Of course setting up the missions to be in line with the reward is a pretty daunting task in itself.
Plus, the unique missions are pretty time intensive (modding wise) when you consider the gameplay gains. And if you put the unique enemy in a regular random tileset, much of the 'uniqueness' is lost. If done this way, most of these missions would work exactly like Zaxx's Assasination mission.
