The thing about Angels/Stone is that other than the very basics of the race, it radically changes the Angels, both with a bunch of retconned in abilties (some of which, like the image of an angel becomes an angel, could well have serious implications for the protaganists of Blink) and modus operandi. The Manhattan episode, while having it's own flaws, at least builds on the angels and makes them scarier by focusing on what's already established.
Worst of all is the change to how their "quantum locking" or whatever is portrayed. In Blink it's said that they absolutely cannot move when being observed, so the turning to stone must happen by unconscious reaction. However, in that case, simply acting like you're not blind shouldn't activate the abilty, they're not actually being observed, so the reaction doesn't kick in, period. Amy's fake-out only makes sense if they choose to turn to stone, which means a bunch of times when they were inches away with nothing to stop them, they just decided to freeze. Blink also had the nice touch that it treated the camera observing the angels for that as well, which they just tossed out in the two-parter.
Fair enough on the vampire/werewolf thing.
As for the Daleks in the season 5 finale, they seem thrown in because there's no reason given that they, being the fanatical space nazis that they are, would decide to work with a bunch of inferior races. They'll happily die rather than be corrupted, and ending reality has been on their list of goals as well. The utterly lawful Judoon being in the alliance as well is similarly strange. And honestly, the River making a Dalek beg for mercy is one of those things about River in the post-RTD era that makes her "meh" to me, special pet treatment.
To be fair, it's not like I despise the more recent Doctor Who, or even season 5. It's still pretty solid in general, I just think Moffat worked best as an episode writer, as showrunner he seems to get caught up in something that seems cool and not uncommonly ends up ignoring continuity or leaving threads dangling. And while RTD did some good work, Love and Monsters was definitely not one such episode.