I don't run separate networks or subnets here, and don't have any problems of note mixing and matching jumbo frames -- I guess path MTU detection is doing its job. The only "internet" problem I have is that I can't get to my (non-JF capable, GbE) router's web config page when JF are enabled, but there's a simple fix here -- click on the web page 3 more times, wait for timeouts, and then remember "oh yeah" (j/k) and disable JF on my NIC or change to a computer that doesn't support JFs.
The problems I have with JFs are more subtle -- spending time and energy in obtaining devices that actually support JFs at decent sizes, dealing with the occassional performance loss accompanying jumbo frames, and often finding after this effort that the returns are marginal.
Returns are significant when I'm dealing with PCI NICs at high bandwidth, or with high CPU utilization, thus it's worth the hassel in some cases.
But I think I have to agree in general that the potential minuses aren't worth the potential plusses in many cases, hence the comment about JFs being overrated.