The problem is worse for E-Ink than for "legacy" devices, in part because they are new and in part becase of deliberate policies of the vendors.
For non-DRM e-books, FBReader demonstrates that one technical way out of the "The Tower of e-Babel" is simply to support every format with a published spec and a wide enough following (the only exception is PDF, with some formats on the to-do list). FBReader only runs on Linux, but every single E-ink device so far is also Linux under the hood. MobiPocket takes the slightly different approach of converting several formats to its own format, e.g. on a Windows PC, and then exporting the resulting file to the reader. Note that MobiPocket may natively support your .prc files. Either approach works, and in effect the Sony Reader community has been forced to adopt the "conversion" approach - but in an ad-hoc fashion and without the inside knowledge that the vendor (Sony) could bring to the effort. Third party conversion tools are valuable additions to a vendor's own tools, and some are of very high quality. I sometimes have to convert a file to fix minor issues with FBReader's rendering for example. They really shouldn't be the only option for mainstream e-book formats and mainstream e-book readers.