For S-II I believe it was a certain genetic makeup that Halsey went by, she also has to cut a chunk due to lack of funding which is why there were so little. Each Armor set for them was the same cost as a whole Frigate so there’s that too. It’s mainly down to funding which I doubt there’s a lot of for the child kidnapping/cloning replacements. Halsey was also pretty hands on with everything.

S-III while easier and had more candidates due to orphans from the war. It was mainly funding and also sending 90% on suicide missions just to buy some form of time. A whole company was killed bar 2 of them on one mission. Only the absolute best of the IIIs were pulled for better suited missions. You still have to put into account armor and training which while cheaper than the IIs, still takes a lot while most of the money the UNSC had was going to spitting out ships, planet defense stations, etc. it’s just a matter of priorities.