I have not read enough fanfiction to know if it reads like fanfiction, but then I haven't read much fanfiction because I have not wanted to do so.
I have an interest in popular fiction. When I was younger, I avoided such things, thinking myself better than that. In all honestly, I still do. I'm an elitist, I admit it.
That is one of the central themes of popular fiction. The protagonist are usually special, in some very special way. The boy who lived, or the sole expert in all the necessary fields, or the prophecy come to fruition, or even the Librarian. In the case of Ender's Game, the protagonist is a supergenius. The supergenius. In a school of supergeniuses, the protagonist makes them all look like idiot monkeys.
Now, to counter that, there needs to be some sort of humanizing weakness.
The key point of that is humanizing. Ender has very few of these, he's younger and smaller and so he compensates for these and uses them to his advantage. He has compassion, we are told, and makes a habit of feeling guilty for the people he hurt, but it is less compassionate humanity and more chronic depression.
And that, I believe, is the real beauty of Ender's Game. Whereas most popular novels try to appeal to and intrigue the average reader in some way, this novel seems more interested in latching on to the ego of the reader and creating a co-dependence. It appeals to the reader's sense of superiority, lays down the most basic stupidity as being of genius-level, so the reader feels that much more intelligent when - like the protagonist - they figure it out easily. There is no challenge to it. Were the games in the book real, i suspect the author would not be very difficult to defeat.
We are expected to take the word of the author for most things. His characters can discover the secret truth of things for themselves, but the reader must take the authors word for it. There are no examples, no subtle hints or clever patterns, just author telling you. A character is not seen doing intelligent things, leading the reader to recognize their intelligence, instead the reader is told the character is a genius.
As previously mentioned, I believe that one should make the best decision they can at the time, and if they have done so the result is somewhat unimportant. In popular novels, the characters usually make unexpected choices that miraculously turn out in their favor. Ender is an extreme example of this, because in the things that matter, he remains undefeated, despite being young and virtually untrained in military tactics. Not just more wins than losses, not just winning when it counts, not just the best of his year, not just the best ever, but undefeated at anything. Not even Paul Muad'Dib, at the height of conquering the universe, would have attempted such a claim.
And then we come to the ultimate piece of the Ender puzzle, which is that every aspect of his life is the result of an all too human supernatural power, which takes ample opportunity to Godlike state that he is causing all the bad things in Ender's life out of love.
Oh, and takes every opportunity to state that Ender is smarter, stronger, and better than Him.
Thus appealing to the sense of superiority as well as paranoia.
There are numerous references to religion, for no real purpose, except for the possibility that they are trying to make it clear that Government has replaced God.
There are numerous other pointless references, and because of the way they are told, this includes the conquest of both the planet and (separately) the known universe.
Anyway, I don't think it is well written, but I can see how it makes an impression. If I had read it when I was younger, perhaps it would have made an impression on me as well. And then a few years later I would have fallen in love with Ayn Rand's writing, and grown up to be a somewhat different person.
I think I am a better person than I would have been.