I suspect this is how they caught the Silk Road guy. Tor is likely entirely transparent to the NSA, just from metadata. It kills me to see articles like this one recommending running a Tor node. I ran one for a while after hearing about it's use to avoid political oppression, but the traffic, from my reading of the meta-data, was dominated by video downloads. In theory, Tor is about freedom, but in reality, it's about porn.
It is 100% possible to provide the kind of freedom Tor in theory was created to provide. First, do exactly what you said, and eliminate the meta data leaks. So long as the network is used to provide freedom rather than illegal video, the bandwidth per volunteer node will be very low, even with the techniques you describe. Freedom is about basic communication like accessing email lists, not watching 2 hour videos for free.
The second part is insuring your bandwidth is used for goals you support, like freedom of expression, rather than the crap Tor is used for. This can be done with "secret identities", as in Super Man and Spider Man. Each user would have their actual identity protected as a secret, while their "public" identity would have their network behavior, such as which web sites they visit, documented in a public unencrypted P2P social network. This would allow individuals to safely collaborate on worthy goals, while keeping illegal video sharing goons from wasting our bandwidth.