The reason to read a digital comic frame-by-frame is because you can. I don't like when frame-by-frame prevents you from seeing the whole page because there are some aspects that get lost when you never see the whole page of panels, but frame-by-frame is great if you're using a device that's smaller than the iPad, and it also makes it easier to focus on individual panels. When I use frame-by-frame mode, I notice the art in general more and pick up more of the details.
But that's something you only get with new comics, bought through the app, like ComiXology. The OP wants something to read the files they have, and those can be read a page at a time or not just by using the zoom function and an appropriate reader.
If the OP has a Mac, then another program to look at is ComicBook Lover, which is both a cataloging program for your digital comics and a reader for iOS. The thing I like about it is that you can put all kinds of data into the desktop program, and some of that data will still be available in the iOS reader. Unlike ComiXology, which uses file names to guess at series and numbering, ComicBook Lover takes that info right from the desktop application, so it doesn't have to guess. You can also browse your collection other ways, like by genre.
In spite of this, I've migrated to Comic Zeal. It was a little prettier, and to get the full benefit of ComicBook Lover, you had to use their wifi import program, whereas Comic Zeal can get the comics through iTunes. Also Comic Zeal lets you organize your files on the device in a number of ways. Unlike one of the previous posters, I have no problem getting .cbz/.cbr files from my Dropbox and selecting, "Open in Comic Zeal" as a way to import comics on the go, but usually I do it through iTunes. I like what I'm hearing here about Comic Glass, and I may have to check that out, too.
I think the iPad pretty close to perfect for reading comics. The screen size is close enough to page size that I can usually read comics a page at a time, but sometime the type is small and/or the resolution isn't quite high enough, and I have to zoom. Fortunately it's easy enough to do, and probably not even necessary with the newer iPads. For Manga, which seems to usually use a smaller page, the iPad will probably be even better.
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