I personally my preferences are.
PDF designed for my reader > ePub > PDF not designed for my reader
I've even taken PDFs, converted them to ePubs, and then converted the ePubs back to PDFs made for the dimensions of my reader in my preferred font/font-sizes.
But it depends a lot on what you read. If, like me, you read technical articles containing mathematical or other symbols, PDF is pretty much the only game in town.
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