I’ve been using Manga Studio EX4 for my comic pages. Pages and layouts are more manageable in Manga Studio than they tend to be in Paint Tool Sai or Photoshop; however, the coloring tools could be a lot better. Most users I’ve spoken to tend to use Manga Studio to create their line art, and then export the page for coloring in another program.
Manga Studio 5 was released recently (at the end of last year), and it attempts to fix issues with coloring by adding in more standard coloring tools, as well as more detailed brush settings. Most of the features from EX4 are still here, though moved about in the switch to a new UI. The only two major features that appear to be missing are story files, and the ability to draw pages at greater than 600 DPI.
It’s easy to get confused, even if you’ve used previous versions of Manga Studio, since panel rulers are now hidden under the Figure drawing tool, and perspective rulers have been moved under the Layers menu.