IIRC that secret project was introduced fairly late into the development to help with one faction which had a horrible probe value(Gaians?).
Not that it was a good design decision, that is.
Probably the worst design idiocy I've ever encountered has got to be either:
a)Oblivion's level scaling, everything scales to your level, except it isn't to your level but some arbitrary power level a developer or a tester has thought sufficient, which means around 80% ALL character builds are gimped and cannot survive after level 10. Fortunately, Shivering Isles didn't suffer so much from this. I pray every day for Fallout 3.
b)Save point system past the year 2002, we have hard drives in consoles as of -02 and Xbox, so why the ****ing hell? Why does every darn jrpg force me to track back to save point every time I want to just stop playing for a while? Genre traditions? Eat a ****.
c)Defender bonuses in (old)Civ games. I really don't want my battlecruiser to be killed by a smathering of archers and men in lion pelts, just because they happen to have favorable terrain and city walls. Call to Power anyone?
d)End bosses and autosaves: Hello FarCry and helicopter battle on a sinking freighter! That game had the most inconsistent difficulty level ever anyway, though.