I've got an iPad Pro 12.9 and an iPad mini. I suspect that a lot comes down to a combination of your reading eyesight and whether or not you find the larger screen harder to hold. I like the big screen since it allows me to read full page PDF's without reading glasses. For normal ebook reading, where you can adjust the font size and have the page reflow, the extra size doesn't really buy you much.
Normally, I would recommend going to an Apple store and doing a side by side comparison to see which suits you best, but I guess in these times, it's going to be a while before you can do that.
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