Yes, Magento has its downsides. But, on the upside, their template system is in SOME ways more straightforward and easier to use than either STS , BTS or ATS.
There would seem to be cleaner separation of business and display logic in most cases and the scattered nature of the file locations seems to be the worst aspect of the system - other than perhaps its terminology. But, on the bright side -- at least they TRY to explain it.
David