The difference between Comic Workshop on 3DS by Collavier and Let's Manga on Vita by Granzella is that Let's Manga uses 3D models for the comic characters. Going by the trailer, you can place characters in a scene, like staging a movie or using Photo mode in a game, and can rotate and move the camera, re-position and change details about characters, and add qouteblocks or thought bubbles and speedlines or other effects, all in order to get the perfect panel. Everything is stored as an object placed in each panel, so you can always swap out a background or redo sizing without having to "redraw". It then "imprints" the graphic with hashlines and halftone as if it's a 2D page.
Comic Workshop is a more traditional sketching app, with some simple panel layout templates to help you design your page and then a few tools to empower your illustrations. It does have layers (which can be shifted even in the middle of illustration) so that you can work on characters or BG elements in a scene. And it does have a Photo feature for adding graphics into your comic. There's also a publishing model (including JPEG output), which we don't know yet if Let's Manga can do.
Both apps are nice to have, no need to pit them against each other. I would say Let's Manga would be significantly easier to use for various skill levels of creators (depending on what stock material is included in the character set and how much customization is allowed) as you just place characters and have fun. You could improvise a comic and find surprises in moving things around or adding fun effects. Deeper comic design, however, and variety between comic panels may be a real challenge for this application. Comic Workshop is much more dependent on an artist's ability to sketch and illustrate, you will always start off with just a blank screen, a few panel choices, and (hopefully) an idea of what you want to make. If you are a great artist, however, the sky's the limit. Either one can be used to make something fun, it just depends on what you're looking to make. Most people will side with the pure drawing app, but the accessibility of the 3D apps has its appeal for like web-style comics or other ideas.
This seems pretty cool. It's definitely something I'd mess around with on the side. I'm already currently working on my graphic novel, so I doubt I'd be doing anything serious with this one, or the 3DS one, but I'm always down for some niche stuff like this!