The purpose of the special projects is to provide another method of getting fleet credits for members of large fleets. For a large fleet, getting fleet credits can be a real problem without those special projects. As an added benefit, the limited time projects add some decorations for the starbase.
I know because getting that 10% better performance from a fleet ship is so pivotal to a great STO experience. Cryptic could more wisely spend it's dev resources on better customization options for ship interiors and adding more options to the character creator. They could also just have fleet defense missions give credits and marks.