It depends on your tastes. I don't use the alternative readers, I'm happy enough with the stock reading functionality [well, after doing some minor modifications, particularly AutoShelf for navigating books in a folderesque fashion]. If you don't like the stock reader of course the koreader,coolreader alternatives might be a huge bonus for you.
What's your issue with the web browser? You have to select it once via settings->beta features but then it's a tile on the main screen (as long as you use it from time to time). Also the browser allows setting a custom start page, so if you go to your local calibre server once and set it as start page you should get it directly next time you start the browser.
Webbrowser is quite complicated, I don't think an alternative exists.
As for me, I upload books wirelessly (via my WebPortal/FileManager addon) but it still needs an USB plug for the Kobo stock firmware to actually detect the uploaded books...
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