Normally I just use Koreader on my Kobo. It crops out the margin automatically which is necessary for the small screen. Then I play with the contrast to make the blacks look like they would on paper. Hate asking people to sell their hard work to me but is there something else that this tool does to make the experience even better?
The main audience of KCC doesn't have access to the powerful features of koreader, but filesize optimization is pretty nice and can get filesizes down significantly.
Cropping whitespace between panels (not just margins on the edge) is also cool. And page number cropping.
This is a huge deal for me, last time I wanted to read manga on my kindle the filesize is what killed the idea.
I got around this with Pillow and Python by reducing the image quality to like 20% which in my case didn't have any compromises, but reduced the image size quite substantially. Then I repackaged the images back into cbz and used KCC to make a proper file. As a disclaimer, I have done it only with the Kaiji Ultimate Survivor series to be able to fit the entire manga on my Kindle PW3 with 4GB of storage (I already used up like 1.5GB). Kaiji has less complex drawings, which most certainly plays a role.