I2p can't really work well on a per app integration basis because it requires uptime to be able to make connections. It doesn't have a centralized database of all of the nodes like Tor has. It has to discover them. We're unlikely to see per app integration for this reason.
Really though, apps allowing routing traffic via SOCKS for both Tor and I2P is more ideal than every app having their own Tor daemon. This way you can ensure Tor is updated and has appropriate settings, you don't have to trust each apps implementation.
