That's because Moffat only thinks of them as a joke and only uses them accordingly. It's no coincidence that their best episode was the one Moffat didn't write, The Crimson Horror, and what helped is that Mark Gatiss didn't treat them as only a joke.As for the Paternoster Gang, I think Moffat has pretty much said that there are only so many man-eating lesbian lizard-woman jokes you can make before it gets old.
Yes, they are humorous and work best in a light-hearted episodes, but there's so much more you can do with them beyond the 38th joke about Strax messing up gender identification.
Why not? That's exactly what they did in Time of the Doctor and Hell Bent.As for the Weeping Angels, I think it's a bit more likely that we'll see them again. Even if they had to ask for permission, I think they'd get it. After all, Russell T. Davies creations such as the Ood, the Judoon, & the Shadow Proclamation have reappeared multiple times during the Moffat era. I suppose the one tricky thing would be finding ways to fit them in. Because of their specific nature, you can't just throw them into the background as random aliens like you can with the Ood & Judoon.