Well, if we are being real, rational fiction = "stuff like HOMOR", because that's what I came here to find, and I think many other did to. (although I have found The Bluer Shade of White on HN way befroe I knew what HPMOR was, so that when I've found out that they are connected it blew my mind.)
So I think that the best way to analyze rational fiction is to analyze what I loved about HPMOR:
It was hilarious. I'm a huge fan of comedy, and comedy in HPMOR is really clever. I laughed at Harry meeting Draco scene harder than I laughed at anything else in my life. Lliterally. I had to drink some water and breathe heavily for like half a minute to calm down, that was hysterical.
Theme - science, technology, rationality. And Harry Potter. EY combined all of my favorite things in the world into one book.
Harry is a brilliant, strong, darkish character. He(and Professor Quirrel) is a combination of the best from all of my favorite characters - Walter White, Sherlock, House, Barney. He is as awesome as I can imagine person being, pretty much the definition of what I want to be.
Breaking Bad - style elaborate plots, I love them. Same reason I liked Prison Break. And Martian. I love seing clever elaborate plans being executed. All the munchkining and exploiting everyone else here mentioned.
When I was 12 years old I fell in love with Hermione/Emma Watson =)
So basically EY combined all the coolest things I ever loved or am aware of, and put it together into one book. I later found out that he is also am AI researcher, and I'm extremely interested in the subject.
So I love this sense of kinship, that there are people who think like me, and like the things I like, and got so good at doing things I dream about doing.
Also, rational fiction has the overwhelming sense of "sanity", of very clear thinking, which is so amazing to witness. I felt like everyone was crazy, it was so aweaome to witness a person thinking the way I expect a human being should be thinking.