With english books it doesn't really matter (for me).
But Mobi is quite annoying for german books, since the german language has a lot of words which are very long (not just
compositions, even normal words) and Mobi files can't use full justification in these cases. But this works with Azw3 now.
On the other hand, you sometimes get errors with the table of contents when you convert an Epub to Azw3 in Calibre. And some Epubs can't get converted into Azw3 at all (mostly extreme large files with thousands of pages).
And another problem of Azw3 is that files get too large now. I have some simple 300 pages books that have 4-6 MB now. (Keep in mind that we only have 1 GB on a Kindle.) It would be nice if there would be a waya to get rid of embedded fonts with one click when you convert Epub to Azw3, for example. Most of these fonts don't look good at the Kindle anyway.