The wifi is good for over the air updates, browsing and Wikipedia lookups, and connecting to Calibre's content server to get books onto your device. Now that Rakuten has bought Overdrive, it may or may not be useful for library access in the future (speculative).
As far as file managers go, check out Koreader. Not something I use (having tried it) but plenty of people here do. Read the developer's subforum for more stuff you can do.
Paranoia^Wconcern over companies' access to ereaders is somewhat common, but relatively pointless if you ask me - just use a throwaway email address and never use it again, if you don't want to hack your device to bypass registration.
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