I don't think this would have much of a difference of ability of the government being able to de-anonimize any site that is trying to keep their identity secret.
It does, to some extent, the security model of i2p is quite a bit more advanced than that of tor, i would say 'next level'.
The things that make me say toe is inherently insecure were addressed in i2p many years ago already.
There have been a few successful attacks against i2p services in the past, all very well documented, iirc none were to blame on i2p itself. (Please correct me if I'm wrong, it's been a while)
I2p is generally faster in regards to bandwidth, more resilient against hidden service attacks and has a much lower latency. I've ran a VoIP server on i2p for a while, which worked great, try that on tor... You'd probably even have to modify your software to be able to work with tor, not so the case with i2p.
One of the biggest 'issues' with i2p is that it's basically a closed darkness, unlike tor which provides 'synonymized' access to the normal web for most of it's (or at least that would be my guess) users. So the goal of the two are somewhat different. I did notice the outproxy on i2p was working again about a week ago, but that's not the networks main goal AFAIK.
Best thing about roughly 90% less trolls than tor.