The first one is Nobody Dies, which says the premise in a nutshell: it's an Alternate Universe where all the major characters who died in the backstory are alive. Some things have gotten better (Shinji is relatively stable) some things have changed a lot (Rei is the love child of Haruhi Suzumiya and Elsa Bloodstone) and some things have gotten much, much worse. (Asuka, Asuka, Asuka.) The whole thing is alot of fun and kickass all around, so it's highly reccommended.
Dark and Edgy Pokemon fics are a dime a dozen, but I really like this one for it's strong worldbuilding. In addition to reimagining the Pokemon Universe as a vastly more dangerous place, it has some fascinating ideas, like most of Kanto having a unstable frontier, a really clever plot by Team Rocket to take over, and the constant feeling that there's far more going on in the world then what Ash sees. The story itself is decent at first, but it really starts to pick up once it gets to Cerelean City and the characters start getting much more interesting. Also, major props for reinterpreting Jessie and James as legitimate threats.