It is rare that an acquisition by a larger company doesn't screw a smaller
one. And this happens not because the parent company has a goal of
destroying what they buy, but because merging two different companies is
really hard, from basically any point of view.
I have worked in at least two companies right after their acquisition by a
larger company, and have witnessed all the growing pains. One company of
the two did not survive. And nobody in the parent company wanted them to
fail, quite the contrary.
So, if someone at Skype is complaining that it became worse after Microsoft
has acquired them, the important bit here is not Microsoft, but the
acquisition.