I actually have a fair bit to say about this, what with having an agent pair dedicated to bad slash. However, I am literally about to head off to work and don't have time to properly explain myself. So I'll start with a slightly old but still interesting blog on the subject:

Why Is There So Much Slash Fic?

As soon as I get a good chunk of free time, I'll put forward my own views on the topic.

Gay guys are rarer than straight guys, and more stigmatized. Most fan writers have had less interaction with gay guys than with straight guys, and gay guys in many places still can't be as open about being romantically involved. That means a straight or female writer usually has fewer real-life observations to draw from. Even a gay male writer might have seen more straight romance in his life than gay male romance.

Many slash writers are cis female. They don't have guy genitalia. If the slash gets explicit, that means they're not writing about something they have daily experience. They simply don't know how things work and, if unwilling (or too young) to do the research, can end up writing things that would make any male reader cringe in sympathetic pain.

The lack of experience with guy/guy relationships, plus the lack of knowledge about mechanics, can lead writers to try to squeeze a guy/guy relationship into a girl/guy stereotype. So one guy becomes "masculine" and the other "feminine", and their personalities change, and explicit scenes are written almost as though one of them were female. Sometimes one partner even gets pregnant. (By masculine I mean male-stereotype--the cultural idea of male, you know, rough and tough and muscular.)

Sure, there are gay guys that are feminine in personality and dating/married to a much more masculine guy, but they're still two guys, and anyhow, there's no unwritten gay rule that one partner has to be more feminine.

But regardless of the existence of such couples in real life, when this masculine/feminine stereotype is imposed on couples in fiction with pre-established personalities, it can throw them way out of character. Characters written as a slash couple are often not written as themselves, but as a seme/uke stereotypical gay couple.

That really bugs me. It's as though these writers think that just because a guy is written as gay, his personality must change to a "gay" personality. But gay people have the same wide range of personalities as anybody else; they're just attracted to the same gender. And if I'm reading romance between, say, Aragorn and Legolas, doesn't it make sense that I'd want to read about Aragorn and Legolas, not two stereotyped cardboard cutouts with name-tags reading "Aragorn" and "Legaolas"?

Audience catering and Author Appeal, of the "1+1=2!" variety.

I wonder if the reason Bad Slash is a separate category at the PPC is because of our LotR origins. LotR has a lot more male characters than female ones, so if you're a badfic writer interested in het you're more likely to create a Sue than write about a canon character. On the other hand, there are enough popular male characters that badfic writers interested in slash can just write about them. The Original Series is also somewhat low on Character Replacements, I've noticed, with Loli!Arwen being the only one I remember off the top of my head. I'm not really familiar enough with LotR to say whether it's a difference between it and fandoms like Harry Potter that are rife with them, or if it's just a case of evolution within the PPC. So the line between Mary Sues and Bad Slash mainly seems to be the presence of a poorly-written OC.

To be honest, most slash I've seen that I'd consider mission-worthy is OoC enough that at least one of the characters is replaced. But I'm not a big fan of slash in general, so it's possible I'm just being overly lenient. I have seen some pretty bad het fics that aren't really Sueish, but most of them don't strike me as good mission material; they're mostly short, sappy, and unmemorable.

that the two types are written in, when looking at fanfiction overall. Why that's the case I don't know. Perhaps heterosexual pairings have been prevalent in mainstream media for so long, fandom got bored and went in another direction in their own stories?

I don't often write romance, but when I do, it tends to be of the Slash variety. I just find it easier to write, for some reason. But if the stereotype about all fanfic writers being teenage girls has any truth to it, it might be because two hot guys is better than one hot guy. Still doesn't explain why I can write it better, though.

...it's because most of the bad het falls under Suefics, so the DMS or DF takes care of those.

Because Bad Slash is a whole Department, while Bad Het is only a division.