I just had this thought while listening to Layered Money by Nik Bhatia; Lightning Bitcoin is Bitcoin, it doesn't introduce counter party risk in the way bank notes and other layers of fiat money do.
Lightning is to Bitcoin what transporting gold by cargo plane is to transporting gold by donkey.
I suspect that in the future, how you transact your Bitcoin will be a technicality, mostly only important to the people writing the software that interacts with Bitcoin.
Hal Finney's idea of Bitcoin banks would constitute second layer Bitcoin:
https://bitcointalk.org/index.php?topic=2500.msg34211#msg34211
Although I don't agree that Bitcoin Banks will be the only way to transact Bitcoin, I do think they are likely to have many customers in the future.