Drosophila Melanogaster has an average generation gap of just under two weeks, meaning about thirty generations in a year, thus meaning about 3000 generations in a century. 3000 does not equal hundreds of thousands.
It should also be noted that the Drosophila experiments are very different than animal breeding, and that animal breeding has an important difference from natural selection in the wild.
Fruit flyologists, as far as I know, have never tried to use fruit flies to demonstrate macroevolution. All fruit fly experiments, as far as I know, have had to goal to study individual mutations to get insight into basic genetics and maybe population dynamics. So it is not surprising that experimenters have never bred anything different from a fly: besides what you mentioned, I will point out that no one has ever tried to breed anything that is macroevolutionarily different.
Now, even if they tried, there would be a big potential problem. When humans breed animals and plants, they have specific goals in mind, unlike natural selection in the wild. If, for example, experimenters wanted to produce, by the breeding of fruit flies, an aquatic fishlike worm of some sort, this may be impossible. Not only may it not be possible to get morphological states in between that are viable, but there may be genetic and developmental roadblocks that would make the goal impossible; you may not be able to get there from here.
This isn't a problem in the wild since there is no attempt to reach a predefined goal. Variations are produced in many different directions; some directions are weeded out, leaving a few successful variants; these then produce young with variations in all sorts of directions, and the successful ones are weeded out. Thus, natural selection "chooses" a "path of least resistance" that may meander around a bit, but may finally reach a state that is different from the original form. And this final form will probably not have been predictable in advance -- I mean, starting with lobe finned fish, would anyone have predicted a descendent like a humming bird?
So what has and has not been produced in a laboratory with Drosophila tells us nothing about what is or is not possible in the wild. Besides, even if something radically different were produced in a laboratory, the response would either be to mumble that it is still the same "kind" despite its differences, or to say that this proves it requires an intelligent designer to produce the change.
I've done everything the Bible says, even the stuff that contradicts the other stuff! -- Ned Flanders
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