Gotta admit, after using Lightning + Bitcoin in the real world; for both trade over the internet (coding/consulting) as well as at a POS (lattes, cookies) - it does feel like two separate systems. You need a separate type of wallet, separate type of address and fixed addresses is not a solved problem yet so unlike Bitcoin you can't just stick a QR on the counter and have people pay you like that. And then explaining to normies there are these 2 different types of Bitcoin is annoying.
These are merely UX and surmountable technical challenges that I assume will get ironed out to the point where they both feel as 'one again' someday but on the other hand if the anti-Segwit crowd got there way I can't help but imagine if we would not already have super (maybe not lightning, but 'good enough') transaction speeds and low fees on the native chain; complete with the benefit of fixed addresses and all the features of existing wallets.
Or maybe now is a good time to take a gander at Bitcoin Cash to see the state of thing there....