It focuses only on being a darknet, whereas Tor focuses on providing Internet access, and is a darknet on the side (hidden services). Thus the largest weak point is no access via I2P to other networks, but they are just different tools for slightly different purposes.

Furthermore, it's easy to run many applications over Tor since it exposes a local socks proxy server, whereas I2P typically requires more integration of the apps which runs over it. Nevertheless, Bitcoin Core has implements special handling for both Tor and I2P, and once the work is done it's no longer much of a drawback.

For anonymizing onion type networks being less used is a drawback, since the network is smaller it's easier to analyze from the outside.