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Given that most/all epub3 readers can read epub2, I do not think you need worry about epub2s becoming unreadable for a very long time.
For most typical, mainly-text based e-books, the only real advantages of epub3 are:
1. enhanced semantics/nav/audio to allow those with disabilities to use automated reading software to more easily read and understand the e-book or listen to any to synchronized audio tracks. But this requires work on the part of authors to annotate the text with semantics tags throughout of add support for audio text synching.
2. better or more complete CSS 3 support
3. audio and video support is claimed but spotty in actual readers especially for video formats
4. support for javascript to possibly "enhance" an e-book (but again spotty support in readers)
5. support for mathml but again this can be spotty.
6. more standardized fixed layout formats but possibly incompatible with Kindle formats
etc.
So a simple conversion from epub2 to epub3 without further work to improve the e-book really doesn't buy you much if anything. It does gain you access to the latest tools such as the latest epubcheck, and possibly the latest kindlegen versions but ...
That said, creating new epubs in epub3 and keeping the toc, should allow for backwards compatibility with epub2 readers while allowing the use of more advanced features if you so desire.
This is all my two cents fwiw.
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