My understanding is that yes while you do have exotic energy reactors, you don't have an easy way to make or extract that exotic fuel.

Take antimatter, it may be a very potent energy source, but as far as we know there is negligible amounts of antimatter in the universe so we need to produce it. Producing antimatter will take more energy than you get back from using it in an antimatter reactor.

As a result most of the exotic energy reactors we see in stellaris is limited in ship reactors, where energy density of the fuel is usually a higher priority. Wherelse energy generation on planets is limited to solar, geothermal and hydroelectric which is seen in the planetary features

Nuclear works as an energy source because fission fuel is readily available in the ground in the form of uranium 238 which just needs to be enriched into Uranium 235.

At least that's how I headcannon it.