Yeah, I used "send to kindle" for a long time and it's perfectly fine for just getting stuff on the device easily (especially since you've got multiple devices and might want to use the Amazon cloud), but there were a couple things about it that annoyed me and got me to switch. The first is obviously that it converts everything to a "document" pdoc file instead of a book (which is obviously more of a psychological thing to make anything not from Amazon seem like "the other"), but the second issue is that the mandatory conversion would seriously screw with the formatting of the book and they just looked worse than their "native" Kindle versions, with weird spacing and big margins on some books and no way to fix it.

Calibre is admittedly kind of a pain at first (not only do you have to plug in your device to a PC, the software is often unintuitive and confusing), but I think it's worth checking out if you're not buying books from Amazon but still want to get the best e-reader functionality out of the device possible (and it's a nice way to see your non-Amazon ebook collection separate from the device). I convert all books to the AZW3 format with it, then use a plug-in called Quality Fix (specifically a function in it called "fix ASIN for Kindle") and it makes all books pretty much indistinguishable from their Amazon counterparts.