I'm so glad the first part doesn't apply to me. My main lead is male, sure, and he so clearly is head over heels for a woman, buuuut she's honestly so dense his advances fly straight over her head and to the moon. I understand how annoying that is. I really like it when they play it up for a joke, though, because that's what it does to most stories - make it an absolute freakin' joke. If done right it's a hilarious romp or, perhaps, is a key point of development for the main lead (I.E. they hate everyone falling for them, use it to manipulate, etc.) but more often than not it is done wrong and just crashes everything to a halt.

And the second issue... yeah. That happens a lot. I'd like to see a story where someone gets beaten to death by a Togekiss. Feel the love! >:D I digress, however, people need to remember that Dark =/= Evil. Sure, I think in Japan it literally is Evil Type... but I like to think they are misunderstood. Go for uniqueness!

My biggest pet peeve is when people have a character be the long lost sibling of a canonical character. I'll cite any character from any video game. People don't try hard at all to write in a character for this. They just show up, no backstory, and they have applause. This isn't too bad for characters that are either minor, but for main characters it's a huge problem. This is especially apparent when that character is never stated to have any siblings or is 100% confirmed to not have any.

An example? I read a story that was a Sonic story. Shadow is confirmed to have no siblings, having been created on a secret base in space. Not only did he suddenly have several siblings, they were all developed on another secret base in space. Oh, and they were all ungodly powerful and switched sides on a dime for no reason.
Spoiler:
Said story also had a lot of rape/sex in it... X_x
This is why I don't read fanfiction.net.

Now, obviously there are issues with the Mary Sue factor here, but that's a topic for another time. It just irks me so much when people break continuity to the point of adding in lost siblings and such. It's just so out of place and shoehorned in... I've rarely seen it done right. When it is, it works extremely well, but most of the time it just falls flat on its face and is cringeworthy.