A question was brought up on HaloWaypoint.com about who created the Spartan I project. The following was my answer to that question. I hope you find it insightful.

The Spartan I program was originally called the Orion Project and only in later years was it called the Spartan I project. Halsey called her program Spartan II after the Orion Project had been commissioned and before Orion had been referenced as Spartan I. She felt those people were the first Spartans even though the program was not called that. ONI was the department in charge, specifically ONI Section-III (the Special Projects section of ONI Beta-5 division).

The Orions however were under the command of Naval Special Warfare command. A specific person running the program has not yet been revealed. Sergeant Major Johnson was an Orion. ONI talked of a disease called “Boren’s syndrome” that made people immune to the flood, though it was really a cover up for those who were Orions. This is why Johnson was not converted to a flood.

You can read much more on wiki, though how much of that is “true” you’ll have to read for yourself and check all of the references.
Here is that link: http://halo.wikia.com/wiki/ORION_Project

Considering the Orion Project started much earlier in Halo-lore, we may never know, unless a prequel game comes out and the info revealed then. (Halo: Insurrection?) Anyway, it’s likely a team effort and credit not given to any one person, though that is just a guess at this point.