I think its called genetics. Even though you can run through thousands of generations of fruit flies in a short time you still end up with fruit flies.
You have described no limitation to evolution with the word "genetics". Go back and describe what process limits evolution, other than time, and the number of generations.
Even though you can run through thousands of generations of fruit flies in a short time you still end up with fruit flies.
You end up with fruit flies that cannot interbreed, and are thus different "species". This is how evolution happens.
There is no "macro" vs. "micro" evolution. It is one scientific theory, with no limitations other than time.