Having said that, there are definite deficiencies. It's fragile in many ways: it shouldn't be possible to launch flooding DoS attacks; encryption should be baked in to all the transport protocols; the ability to connect to a computer should be much more under the control of the recipient (today's firewalls are a poor workaround for a design deficiency). The routing system is pretty fragile.
The ability to handle multiple networks simultaneously, and gracefully move between (or use more than one simultaneously) isn't something that was originally necessary, but is today with mobile devices. We're working on fixing that with MPTCP, but it will take a long time to univerally deploy.
So, lots of architectural issues, but it's important not to lose sight of what is good about the current network too.