You're right that making up any old rule that preserves a favored thesis isn't genius, it's dishonest and certainly unscientific.
I think the best defense of Ptolemy here is (a) the theses he was defending weren't his pet theses, but core conceptual truths at the time. The perfectly circular and uniform motions of the planets, as well as the immobility of the earth were very deeply entrenched; and (b) the discovery of eccentrics and equant points was a remarkable feat of geometry. It's important to remember that they are actual discoveries. Before astronomers went about trying to preserve the Ptolemaic system in this way, nobody knew they existed. So discovering that they do exist gave them a reason for thinking this is what was really going on.
The mathematics of epicycles turns out to have been very important in its own right. It's just not a correct description of what is going on in the sky.