Things are moving toward standardizing the tests, and Total 25-hydroxyvitamin D (D2 + D3) is the currently considered to be the correct measure of Vitamin D status. Unfortunately the standards for deficiency have yet to be established, and they will vary greatly based on a number of things from time of year to complexion...both those things, and many others, have an affect on how Vitamin D is absorbed and metabolized. Having said that, my doctors always test both, at lease for me, possibly because I also have sarcoidosis.
The two tests are used in different circumstances...low blood levels of 25-hydroxyvitamin D may mean that you are not getting enough exposure to sunlight or enough dietary vitamin D to meet your body's demand or that there is a problem with its absorption from the intestines; low levels of 1,25-dihydroxyvitamin D can be seen in kidney disease and are one of the earliest changes to occur in persons with early kidney failure, possibly indicating that the amount coming in is sufficient, but it's being excreted abnormally quickly or not being metabolized properly.
Some disease processes (parathyroid issues, sarcoidosis, lymphomas) can cause increased calcium levels or excess production of 1,25-dihydroxyvitamin D.
There is also a complex "balancing act" of different components that can change the Vitamin D levels...calcium, magnesium, and the actual vitamin are all dependant on each other, and in some cases, it's actually possible to increase Vitamin D levels with magnesium or calcium, not the actual hormone.
There are a lot of variables, and it's most definitely an area that needs more research.