I'm going to start this post by saying I think they're all crap; $cientology, Christianity, Judaism, Hinduism, any and all brands of Neo-Paganism; the whole lot of them.
But there are some pretty clear cultural differences between, say Hinduism and Christianity on one side, and Scientologists on the other. While the former religions may have started out something like the latter ones (though I suspect it was far more complex than some guy sitting down and writing a religion purely out of his imagination), there are literally thousands of years of cultural and theological development behind them. They have had significant a longstanding influences on the civilizations in which they evolved (or were adopted).
Scientology can be traced no further back than L Ron Hubbard telling some of his far more talented peers he planned to create a religion to prove how easy and profitable it was. Unlike, say, Hinduism, which is a historical evolution of the Proto-Indo-European religion, Scientology has no real antecdent, unless you count the self help movement and Hubbard's fetishistic dislike of psychiatry.
Even the early Christians took the Jewish Bible, plopped a second part on it and mixed in some Hellenic philosophy into it, and thus has antecedents dating back centuries.