I too used Aldiko Premium for years, but it's always been inflexible about where books are located and I haven't seen any significant updates in a long time.
I tried Moon a couple of weeks ago after I started using Calibre Companion and find that the two work very well together. I do what @dwanthny does and let CC manage the library and when I select a book it opens up in Moon, and unlike Aldiko opening a book outside of its own data base, Moon remembers where I left off reading. Moon has lots of other capabilities, including fine tuning the foreground/background for best viewing / least eyestrain, and a lot of flexibility in what gestures and/or keys move forward and backward. I paid for Moon within a day after trying the free version and uninstalled Aldiko.