OH HEY, BAY. LET'S BE BFFS.
Seriously, this. I love it when people actually bother to do their homework and write a canon character in-character. It shows off a lot of creativity and care. I mean, all too many times, I've seen kids completely throw out characterization because "OMG IT'S FANFICTION" or "OMG I JUST WANT TO LIVE VICARIOUSLY THROUGH MY MARY SUES" or "OMG IT'S ARTISTIC." But all that does is make the author seem intensely superficial because the characters are only the same in name and maybe design. As in, their personalities and backstories are chucked out, so who are they besides hand-puppets? It's a lot more interesting (and challenging, for that matter) to figure out who those characters are and work with their personalities, not throw them out. Preserve the characters to show how dedicated you are to them and bend your sense of creativity to figure out how to make a story interesting without violating who those people are. Doing that shows that you actually care for them on levels a lot deeper than "hurrdurr this character is hott."
Double points if that canon character you're using is a random side character, and you still get their characterization right. No, saying "Pokémon doesn't give characters much in the way of personality" is not an excuse. The writers gave us enough to work with, and anyone who uses this as an argument is immensely lazy.
Also, interesting original characters. Characters in general, really, if they're actually deep and human and do interesting things besides talk, have sex, and/or angst a lot. Characters that make sense and struggle. Characters that aren't exactly Chosen Ones destined to save the world but somehow caught up with the entire storm that is the plot. Characters who aren't over-the-top angsty/cutesy/macho/whatever or stereotypical in any particular way. It's hard to describe in words, but I love it when characters are actually good.
Plot's a big factor too. As I've said on the other thread, I loathe bandwagon fic, but if it's clear that your fic brings some new and interesting ideas to the table, I'm all for it. More than that, I gravitate more towards plots that excite me. Like I didn't say on the other thread, spending paragraphs to describe a set of curtains is not going to thrill me. Building up suspense for reasons I can clearly see and leading into a plot where characters actually do things (that make sense) will.
And of course, formatting. Superficial, yes, but with the number of fics that have murdered my eyes, I'll happily sit down to read anything that doesn't give me a headache when I try to tackle it.