I'm reading Dune at the moment and really loving it. Not sure if I'll continue afterwards or not... part of me thinks not, but I see some people really love the later books. I've been warned not to read past 6 (Frank's last books), and that 4 is a better stopping point since 5&6 are an unfinished arc. Then some people argue just 1&2, 1-3, or stop after the 4th.
The thing about Paul being a mary sue, it's really more about perception because every fiber of his being has been prepared to fill a very particular role. He's also not entirely without flaw and he's not exactly someone you'd want to step into the shoes of.