I've often repeated that I see no reason why I, as a reader, shouldn't hold fanfiction to the same standards as original fiction. But the fact is, most people do evaluate pony stories (or any derivative stories, for that matter) much differently than they would commercial fiction. Why is this, and are these differing expectations fair to both author and reader? My thoughts, below.
The fact is, most people don't expect a lot out of fanfics. I'm not just talking about the non-fanfic-writing or -reading masses who look on derivative fiction with anything from bemusement to downright hostility, but about people who read fanfiction on a regular basis. Glaring problems in writing, editing, and story construction which would be literally unimaginable in commercial literature are regularly accepted without comment by readers who would not hesitate to cast aside a paperback with a mere fraction of the issues plaguing the fanfic in question.
One of the reasons readers, as a group, tend to be far more forgiving of fanfiction than they would be of original fiction was recently discussed in this A.V. Club article discussing podcast reviews: fanfic authors work for free. It's easy to look at a ponyfic author and say, "this guy's just writing in his spare time, it's not fair to expect him to write something great." After all, you wouldn't berate a youth soccer team for not playing as well as Real Madrid, right?
That's true, insofar as it goes, but it misses what seems to me to be a crucial distinction: the author isn't the only person with expectations. The reader's experience counts too, and it's the reader's experience that the reader should be primarily concerned with. And in terms of my enjoyment of a story as a reader, it doesn't really matter how much remuneration, if any, an author is receiving; a good story is still a good story, and a bad one still isn't. To pick the sports analogy back up, youth soccer is a great learning experience for the kids, but there's a reason the crowds at those games are mostly parents and other family members: people looking to enjoy watching the game (reading the story) generally prefer to see a top-tier team at work.
Another factor contributing to the lowered expectations is the tendency to compare within overly-restrictive sets. When someone reads a fanfic, their natural inclination is going to be to compare it not to the books they've recently read, but to the fanfiction they've previously come across. Since there's no barrier to entry with fanfiction (quite literally, anyone capable of stringing words together can present their story online if they wish), mediocre stories can seem disproportionately wonderful by comparison to the sludge around them.
But the fact is, fanfiction and commercial fiction both compete for the same resource from readers: time, and specifically time devoted to reading for pleasure. Time spent reading fanfiction is time that could be spent reading "real" literature, so why waste it on something subpar?
I'm aware that, to this point, it probably sounds like I'm making a case against reading fanfics, but that's not true at all: I love fanfiction. I love writing, I love reading, and I love doing both in regards to FiM. I simply don't see why I should automatically love something because it's fanfiction, as so often seems to be the case among otherwise discerning people. I expect any fanfic I read to be interesting, engaging, and to generally justify the time that I invest in it. Any author who posts their story publicly (as opposed to writing for oneself or one's friends/family, which is a perfectly valid hobby, and one which does not require posting one's story to FIMFiction, FF.net, etc.) is implicitly asking that it be read, and I don't think it's unfair to ask of them as much as I ask of any author, commercial or not: don't waste my time.
In fact, I think it's a disservice to take the opposite approach: to "generously" expect less of a story simply because it happens to feature setting or characters from a previously existing work of fiction. To do so discounts the possibility that a fanfic author could write anything worth reading on its own merits, and to disprove that idea is as simple as looking back at some of the stories I've reviewed for this site. Refusing to hold flaws against a story because it's "merely" fanfiction at once discounts wonderful stories like Memories of Those Friends Who've Gone Before Us or A Cup of Joe.
There is no inherent reason why a fanfic cannot be just as good, by any literary metric one cares to use, as a given piece of original fiction. I think it's only fair to recognize that, and as readers to ask of fanfiction exactly what we ask of commercial literature.