Eww, no. PDF is not a valid ebook format. Ever.
All of the bullet points you called out in favor of PDF apply to other, better formats like epub. What you completely missed, however, is that ebooks need to be scalable. The PDF you create targetting your Kindle may look great to you. What about someone who wants to read with a smaller or larger font size? What about someone with a smaller or larger screen?
PDF is a print tool. It's great for pixel-perfect layouts at a designated size. AKA, a printed piece of paper. Ebooks must be more fluid.
You remind me of "web designers" who have come from the world of print. They always want pixel-perfect pages designed for a browser running at 1024x768. Deviate from that in the slightest of ways (increase your font size, change the size of your browser, change the size of your screen, turn off images, apply a user style sheet, etc) and the whole experience degrades into a huge steaming pile.
Ebooks are to paper books as the web is to magazines. What works for one does not and cannot work for the other. The web is resizable and flowable, and a good designer takes that into account with fluid designs that adjust gracefully to the user's preferences. Ebooks must also be resizable and flowable, and PDF is the wrong format to support that.
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