Funny you should mention fruit flies, Laura.
For it is with them that some of the limits of mutation and genetics have been shown. This
link is a bit over the top, but it gives you the idea. Evolution in the laboratory shows only very minor changes with some very definite boundaries.
Here 's a site that's a bit less extreme.
And you are not distinguishing between
microevolution -- which has indeed been demonstrated both in the lab and in nature -- and
macroevolution which has NOT. And it's not merely a question of time. There are fruit fly strains that have been bred in labs for thousands of generations.