@catsknit: I think you are looking at this the wrong way. The question is really, what do you want?
In my opinion, the best thing to do is to put some books on the device and read. And explore the device while you do. Then, when you find a problem, or something you don't like, search the patches or ask here to find a workaround. There are far to many patches/hacks/workarounds/utilities for us to blindly suggest something as a lot of this is personal.
As an example, JSWolf has listed the patches he uses, but, I use none. I do have a couple of the hidden options enabled, but don't usually have the function they enable turned on. A lot of people refuse to upgrade the firmware if the inverse video/night mode doesn't work. But, it isn't something I like at all.
The epub vs kepub is another personal thing, but can be affected by your reading matter. If you read books with a lot of footnotes or images, then kepub is the better choice. But, if you are reading reading fiction with simple formatting, it probably doesn't matter. But, again, some people hate the header that kepubs display.
Overall, this is your device and you need to customise it the way you want it. You can't really "trash" it. The worst is that you would need to do a factory reset and start again.
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