As I reader, I like both. But how much I like a comic (aside from story and artwork) usually boils to a few things:
1) Readability!
2) Art Flow
I HATE it when I have to squint to read tiny text or if I don't know which order to read panels. Just makes me frustrated when reading. As long as you have those two things and a good story, I could care less about the format. However, using the chosen format's full potential is always a bonus.
Now as a creator, again I have to say both. Starting out, I was really against the vertical comics. Especially since I was used to learning about and using page-by-page. But after reading a couple comics where it's used creatively, I've warmed up to it and now most of my webcomics are made in the vertical. I don't know, I kind of like the idea of having a little more control what panel the reader will read next.
Course if you plan on printing your comics one day, you could make the comic page-by-page and then format it for vertical when posting it online. Jason Brubaker has a video that explains how he does it.
All in all though, I think it's important to experiment to see what works for you.