The X-Files is more of a problem, because (much as it pains me to say it), Scully is not as well-written/acted as Toby- her character just doesn't have as much depth, thus there is a much finer line between OOC/IC for her. (Hoo boy, now I feel guilty for betraying one of my Big Fandom Loves... *sigh*)
Another thing is, whether you're using your own characters or not, fanfiction *is* writing, and the more you practice writing, the better you get at it. Some may argue that you don't get any practice writing characters, but I would disagree (for the reasons stated above). I've read some pretty awesome fanfiction, by authors that, if they wrote original fic, could probably get published at one time or another. Writing good fanfiction, like writing good original fiction, takes time, hard work, and talent (not that I would know from experience, considering all the fanfic I write I keep inside my head).
So... yeah. Lay off fanfiction, people.
(And if I were actually more eloquent than I am, this would make more sense, and contain much less bad grammar.)