I've read some stuff about the next generation internet initiative, and they make the right sorts of noises, but I know @aral is skeptical about it.
I suppose if anyone can get funding from this to do something good and without too many government strings attached then so much the better.
I think I am post-postSnowden at this point. Yes there is a lot of broken stuff on the internets. Yes it needs fixing. No there are not many folks actually interested in doing that because it's not jam packed with smoking hot buzzwords. Companies certainly aren't interested in fixing any of it. Plus it takes some level of knowledge about crypto, and that, which is not all that common.
If there's one thing we could do to improve the internets within the next five years, and if we had a stack of cash (unlikely scenario), going all-out for municipal mesh might be the best plan. ISPs would fight us like rabid dogs. The four horsemen of the infocalypse would be constantly invoked. It would be a bitch, but I think with enough resources a lot of progress could be made towards democratization of the infrastructure and fixing many of the security problems.