Some would say that's the way to do everything. But it doesn't exactly make it easy for the average Joe.
And that's kind of the point too. Police behave badly more often when there is a network with 500 people on it because they don't really understand it and nobody is paying attention to anything. But when there are only 500 people on it, the 500 people can all be using five proxies and blockchains and credit default swaps and whatever else.
Meanwhile by the time it's popular enough that Joe wants to use it, it's also popular enough that Inspector Clouseau is no longer on the case by and large.
But I don't buy the argument that it's targeted just because it's too small. No matter how many used Freenet, it would get targeted because it's way too laid back about child porn. Sure there's child porn on Tor onion sites, but it's not so easy to find, since the Hidden Wiki has been cleaned up. On Freenet, however, it's a top level category on one of the featured search sites.
Me, I'll run my Freenet nodes in anonymously leased VPS, and access them via Tor.
But actually, I won't, because there's not much of interest there.