If my uncle and I both got our DNA tested and compared ancestry results, should we have 50% or 25% similarity? I get normally it would be 25% but since the mitochondrial DNA and Y chromosome are (mainly) used to figure this out using the test we did, shouldn't we share the same exact maternal DNA since it's my mom's brother and that doesn't recombine or anything and they got it from their mother? I just want to know if this is a different genetics problem than normal. Thanks!
The coefficient of relationship between you and your uncle is 25% (see wiki > coefficient of relationship for more info).
However, the percentage of similarity depends on the genetic diversity in the population of interest. If you were studying a population of fully homozygous clones (no genetic diversity), then no matter what the coefficient of relationship is between any two individuals, they would still be clones and therefore perfectly similar.
Usually relatedness is described via the coefficient of relationship because it is natural, relatively simple to calculate, and corresponds well to the actual amount of DNA likely to be inherited. In this system, you are 50% related to your mother, and your mother is 50% related to her full brother (your uncle), so you are 50% $\times$ 50% $=$ 25% related to your uncle.
This measure is an expected value, the average amount of DNA inherited across a large number of instances. A particular instance can vary from the measure due to randomness in the biological process. Although the percentage from parent to child is always the same, more distant relationships are affected by genetic recombination resulting in a bell-curve distribution around the expected value.
The coefficient of relationship matches the biological behavior of the autosomes (nuclear chromosomes other than the sex chromosomes, X and Y), which contain the vast majority of the cell's DNA. The behavior of the X and Y chromosomes and the mitochondrial chromosome differ, however, so this measure does not provide an exactly accurate expected value for all inherited DNA.
"... got our DNA tested and compared ancestry results ... since the mitochondrial DNA and Y chromosome are (mainly) used to figure this out using the test we did ..."
The above pieces of the question suggest a misunderstanding of DNA testing. There are three main kinds of consumer DNA tests: one tests only a few characteristics of the Y chromosome, one a few characteristics of the mitochondrial chromosome, and one tests many characteristics of all the autosomes (and optionally the other chromosomes). The first two are older and not used so much today. The last is what is usually done today to indicate ancestry, and it provides results consistent with the coefficient of relationship measure.