I think any new development around the North Kent line will be compared negatively to Crossrail - as you said, over-provisioning somewhat. I'd steer clear of the river; from QE Hospital (Woolwich Common), continue east through Falconwood or Welling, then south to Sidcup, essentially "bridging" the Dartford lines. I'd like a spur towards Bexleyheath, to give it a new station in a more central location to the current one, but I fear that I'm biased in terms of what would be convenient for myself (or commuters from my area) rather than seeing the big picture. Which, of course, is why I'm not in charge of planning things like this!
For penetration of Thamesmead, a rather fanciful proposal would be to extend the DLR eastwards from King George V or Gallions Reach, with a tunnel or bridge over the river. It would then roughly follow the path of Eastern Way, terminating at Belvedere or Erith. (Or, even more pie-in-the-sky, another river crossing and terminate at Rainham?) Of course, new above-ground construction brings its own problems, whereas this Bakerloo extension would be a combination of new tunnels and sharing existing track.
Edit: the DLR bit might not be so fanciful, my idea seems to be similar to the currently-proposed Dagenham Dock extension!