There are a few examples of M Preg where the reasons behind the pregnancy actually makes sense in the context of story through a scientific or magical explanation. These, however, are few and far in between.
Sometimes can be justified when you're writing about a verse where there are characters that are not human. If the male getting pregnant happens to be an alien species or a youkai, then it could be explained that in their species, males are the ones to give birth.
Fanfiction has to make sense? What? I've stumbled onto fanfiction where it happens for no reason. Two guys have sex. Then a baby comes out. Because gay sex Totally Works That Way.
Sometimes the fic is set in a vaguely Alternate Universe where everything is the same except some scientists discovered X many years ago that some men had the ability to become pregnant.
There's a crossover between the animated Teen Titans and the animated Justice League on fanfiction.net. As per the story, the Robin in the animated Teen Titans is Dick Grayson, and "Teen Titans" take place in the time between Batman The Animated Series and The New Batman Adventures. That's all well and nice...until Batgirl mentions Nightwing. WTF? If Dick Grayson is Robin, "Nightwing" shouldn't exist!
Two possibilities. Dick Greyson was Robin, became Nightwing, and then quit and resumed the Robin mantle.
I don't think it's even stated when animated Teen Titans takes place, or for that matter if Robin is Dick Grayson (even the show's creators weren't even bothered who Robin was).
The Robin in Teen Titans is Dick Grayson (there are several things that indicate this, even though it's not outright stated, the least of which being Nos Yarkcid, Robin's counterpart from another universe). But Teen Titans is not part of the DCAU, which is where BTAS and TNBA take place. So, in the crossover mentioned, it makes perfect sense for there to be both Robin and Nightwing, as there would be two Dick Graysons.
That depends on whether it's really shown as a crossover between different worlds or if it just ignores that "Teen Titans is not part of the DCAU" part.
Peggy Sue and For Want of a Nail fics can be very well done. However, it just seems that too many times, there are a million coincidences that just seem to make everything work out well, which bothers me whenever I try to read one. In Peggy Sue stories, I understand that all of the foreknowledge that the character has helps, but what really bothers me is that, in fics without the foreknowledge, everything just seems to fall the right way. Why do all the problems seem to wrap themselves up nice and neatly and all this screwing with the timeline not cause other, unforeseen problems? This wouldn't bother me so much except for that fact that it shows up in even some of the best written fics of the genre.
The problem with this one is pretty simple - for most authors, Peggy Sue stories are not something that is used not to explore potential character development and moral/emotional/mental issues that something like time travel (whether physical or mental) would cause, but rather as an answer to the question "why is this character stronger and smarter?". And the same thing applies to For Want of a Nail stories - they are supposed to be "what if?" scenarios taken to their logical conclusion, but for most people they are nothing more than a way to somehow show that some character can be stronger/smarter than another character. And they do that because they are afraid; after all, if they really followed the logical implications in those stories, they would have to take them Off the Rails and write their own story as it diverts from the original one, which most authors aren't capable of doing, in large part because it requires knowledge on some topics. Let's use Zero no Tsukaima as an example, shall we? If we got Peggy Sue story in which Louise came back mentally to the time where she summons her familiar, most people would simply follow the original material but make Louise stronger; her emotions towards her familiar would also stay the same. And if the author actually tried to make the story more serious, then Louise would've felt a dissociation from the current situation, and her familiar would've felt differently about her because she would've been more sympathetic towards it from the start; that alone would be enough to change his attitude towards her, and with her not throwing Saito out of her room on the first night, many events would've changed, as there would be no trigger for his fight against Guiche, which means that by the time Fouquet came he would not be aware of his own power, and that is if Louise even allowed Fouquet to steal the target item from the vault. Then, the story would've gone in a very different direction, and the author would've had to have at least basic knowledge of human psychology to know what to do with it. Let's now go in another direction, with Zero no Tsukaima again being the example. What if there was a For Want of a Nail story in which Louise summoned a familiar that only differed from Saito in that he was able to write poems? An insignificant change, however you look at it, but with that simple ability, there would be no reason for Louise to go exploring to get inspiration for the speech, what means that she would not be able to find the Zero fighter before someone else got to it, and Tristania would've lacked its trump card in the first battle of the war. And then the story would've gone to Albuquerque, and to make it plausible, the author would have to know something about politics, diplomacy, and tactics (both field-level and army-level), which is something you won't find in most authors. So, to put it simply, most authors are just too afraid or not skilled enough to change the world significantly enough to match the changes that should've happened because of the initial change. It is easier to write a story where only parts are new and where everything goes fine, than it is to write one where things really turned grim and there is no source material to use to help with writing.
There is also the fact that, the more divergent your fic is from canon, the less likely it will be read.
There is also the fact that, the less divergent your fic is from canon, the less likely it will be read. Who wants read the same story all over again with only cosmetic changes?
When reviewers start their review with, "I don't normally like this pairing, but..." ...So, why did you read the fic in the first place? I said what pairing the fic was about in the summary, so why would you read it if you don't like the pairing?
The Theorem of Narrow Interests-Say you want to read about character x. You usually don't want to just read stories about character x but stories which are 1) readable 2) in a specific genre 3) interpret thecharacter in a certain way, 4) have specific kinks etc. There might not be many new good stories about character x that fit that criteria in your pairing of choice so you might take a look at other stories if they're well-written even if you don't like the pairing because beggars can't be choosers.
There are cases where people read such stories out of boredom, when they read everything else that was recommended for this story, or when someone else recommended it to them personally. And there are also people who read stories that have good character development and merely prefer one pairing over another one, in which case the "I don't normally like this pairing, but..." bit would be closer to "I never saw this pairing as plausible in the source story, but here it is presented in a way that makes sense.". And it kind of makes sense, if you think about it - quality of most fictions is rather low, so it's easy to get jaded when you see a hundred stories with some particular pairing and none of them well-written.
They could also really like the author. Say that an author has written stories about several different pairings, of which you like one, and that's why you originally started reading their fics. If you have read everything that the author in question has written about the pairing you do like, you may end up reading everything else they have written too, even the stories about pairings you don't necessarily care for, just because you love their writing.