As a Baldur's Gate 2 fanfic/novelization writer *shamelessplug*Tale of the Bhaalspawn, go check it out*endshamelessplug* I'd say there's definitely quality stuff to be found out there, but unfortunately, as many have already pointed out in this thread, it's somewhat few and far between. Sturgeon's Law comes into effect big time here- the more popular the franchise, the more craptastic junk you'll have to wade through to find the good stuff buried in there somewhere.Look at the archives on Fanfiction.net- you'll note that the FF7 archive has at present 34,612 stories in there. While I'm sure some of those are good, just how many are probably absolutely terrible?
But to go back to your original question, there's definitely something to be said for deviating from using the main characters in order to create a sense of adventure and drama that the established canon (which everyone already knows and is familiar with) is going to lack by default. Having said that, you want to avoid the self-insert Marty Stu/Mary Sue trap that a lot of original characters tend to fall into. And any exorbitant amount of grammatical and spelling errors will turn a lot of folks off as well. Since you're not using established characters, you don't have to worry about writing them OOC or ruining canonical relationships, etc...
Other than that, it really comes down to your personal preference. A lot of people find different things acceptable or not in stories, and if it's compelling and believable within the established storyline you're creating, go for it.
Will that be enough to escape the label 'fanfiction' and all the stigma that tends to come with it? Maybe not, but like I said, I've read quite a bit of stories that I'd almost consider as good as or better than canon. So yes. I think it can be taken seriously, if that helps at all.