Certainly there's all sorts of quirks including Ethernet collisions. There's variations in switching methodologies, eg who out there is using the new OpenFlow. Also, not all connections are 100% Ethernet either. ATM still has a strong hold. On the Verizon FiOS side, this is one of the differences in FiOS BPON vs FiOS GPON. BPON is ATM based. This applies not just to services like DSL and FiOS BPON, but for interconnects between service providers.
As for Level3's recent statement, no doubt there's a lot of validity. Especially with the statement of:
monopoly rent-seeking conduct Level 3 has observed
Looking at more towards Level3 / Comcast thing - I don't see how in any normal universe Level3 would pay Comcast. - Except in ours of course because that's what ended up happening. How many service providers can Netflix get? Many. How many can the normal consumer get? 1? 2 perhaps. Comcast undoubtably used it's monopolistic powers. If Comcast wants to charge Netflix for a direct connection, that's fine I suppose - Netflix can decline.
The real solution - I don't think is to necessarily regulate Interconnect agreements. It's to ban laws that create monopolies in the first place.
http://www.muninetworks.org/content/big-bucks-why-north-carolina-outlawed-community-networks
There are cities that would potentially like to get a Small private ISP and / or a Muni network which can't.