i agree with the statement that if they had no auguments they arent spartans... you cannot remove the armour and the auguments from the spartans unless you also remove the growth enhancements used on the clones and if you remove that.... i think you get my drift.

from what we know though id have to say spartans would win as they have a much wider gene pool (well anything is wider then 1 i guess :P) this enables them to have a variety of different skills as different people are suited for different things. i.e kelly is a fast runner, john is lucky, someone else is strong etc. the clones are all from the same genetic stock therefore they are more limited in what they can achieve.

 The spartans also have way more combat experience then the commandos and if you read the books they were more then a match for fully trained soldiers even before they recieved their armour and enhancements