The most common reason you are seeing differences in stats after enemy soldiers have been fultoned is because of the 'Boaster' skill. This skill falsely increases a soldier's stats while looking at them through the binoculars. This is to make the player think the soldier in question has better stats when in fact they don't. Once the solider has been fultoned you will be able to see their true stats. After you've upgraded your binoculars to the required level (your iDroid tells you what features each equipment level gives you) you will be able to see what skills soldiers have. Another easy way to tell if a soldier has the boaster skill is if all of their stats are equally high.
Another thing to note is that if soliders are in the med-bay or the brig they will not contribute to your Motherbase's skills until they return from those locations.
Receiving S Rank on missions has no affect on the quality of soldiers you fulton. The rank of soldiers you see within Afghanistan and Africa is determined by your overall Motherbase rankings in each skill category. To see higher skilled soldiers you need to raise your skills to a higher ranking.