Hmm, it is a good idea, but the implementation suggested so far is not.
Naming the embedded port em<number> isn't so bad, other than the fact that it will break a lot of half-wit crap that needs the "eth" as the prefix to know something is an ethernet NIC. Stuff like iptraf, and a great many number of scripts. This is basically unavoidable, and acceptable collateral damage.
But a "pci" prefix for PCI/PCIe-attached NICs? You KNOW it is an Ethernet NIC, at least use a prefix that is not a BUS NAME...
iptables matching is done on prefix (e.g. em+, eth+). You WANT to be able to separate ethernet NICs from other devices by their prefix. Why not use a common prefix for all ethernet-like nics, like, say, "eth"? Sure, give us ethem<number> for the embedded ones, and ethpci<something> for the pci slot named ones. Or ethe<number> and ethp<number>, whatever.
The less said about the idea of using "#", the better. Just drop it, it is a Bad Idea. It adds no advantages and it is potentially hazardous. If you need something at all, use "_" or a letter.
There is no way we'd be able to take that crap naming convention in Debian, but we could certainly adopt the whole idea if the naming was more palatable. And THIS is something we'd all benefit if every distro decided to do in the same way.