Where can I buy ebooks (epub) that give me access to download the file so that I can copy it to my other devices and keep it on my own backups and organize it in my digital library the way I want to? I want a good selection of anime / manga / sci-fi, and a little bit of the typical best seller stuff.
Like you, I insist on having the ability to archive and backup my media, and the second I learned that Amazon was removing that ability I was done with them.
Also just to echo what others have said, I'm of the belief that once you pay for a book/game/etc... as long as you're the only one using it, the rest is free game. Pirate away after you buy a copy and I don't think there's an ethical problem there.
Humble Bundles (if you get lucky and find a good one) are also usually just DRM-free files in a zip archive. I've seen more sci-fi bundles lately (e.g., they had bundles of the complete works of John Scalzi, V.E. Schwab, and Ursula K LeGuin last year), and I think they usually have some anime bundle on offer.
Kobo is also a pretty complete bookstore, and they tend to match a lot of the "1.99 ebook today only!" sales that Amazon runs. I do most of my reading on one of their devices becaus you can sync PDFs/ePubs (via a USB cable or Dropbox) and log in directly to Pocket (for web pages) and OverDrive (for library books).
I saw Bookshop.org also sells ebooks, but their marketing copy ("read right in your web browser, or download our iPhone or Android apps for the full reading experience") makes it sound like they built a closed platform and don't sell files.
Read it on my kindle after removing the DRM and sent it via amazon.com/sendtokindle