Epistemological obstacles for Reductionism

Physics without experimental test is futile. After hundreds --if not thousands-- of years, we have finally settled on some basic quantities, i.e. SI base units. Anything we said and say in physics, ultimately boils down to a mixture of these base units. It is not that we cannot introduce more basic quantities but the epistemological limitations tie our hands very tightly. New basic quantities need not come only in the case of new phenomena. Occasionally theoretical consistency demands introduction of whole new independent base concepts which might not be possible to measure even after having constructed a whole new theory. 

All I want to say is that whatever we want to propose and test should ultimately come in a base units system with finite number of units; but how far can we go here in deepening our basic units? ultimately there is a place where not ontologically but epistemologically we cannot continue to dig down our basic units. we may already be at such boundary. What we can dream of our experimental means to probe is far from what we have in our basic units. 

A related issue here is that of Emergence. Suppose we decide to fix the current SI system as the aforementioned epistemological boundary. in such system a quantity like temperature is a key basic element. how are we then going to explain the emergence of temperature when everything we say in such hypothetical explanation has to be explained in terms of SI base units?!