Using MakeMKV to rip movies works well, you only have to rename one file. When I'm ripping a series where I've got a dozen files in a season things get a little more iffy. I wrote a script for myself which will rename the files in two stages:
First MakeMKV will create a directory based on the DVD volume. Often this is something of the format TVSHOW_S1_D3 - nice and readable as Season 1, Disc 3. The individual files are called title00.mkv, title01.mkv, etc. I run mkv-rename in this directory and it renames the files to TVSHOW_S1_D3.title00.mkv. Now I can move them all to TVSHOW_S1 and they'll be in the right order. But now instead of remembering that I left off at episode 6 I need to remember that it was disc 2, episode 2.
In TVSHOW_S1 I can run mkv-rename "TV Show" and it will try to download all of the episode data from the web and create files like TV_Show.S1E6.Name_of_Episode.airdate.mkv.
It's all crummy BASH scripts and there is precious little error checking (and I can't do things like verify that the files are in the right order so be careful where the extras are). Hopefully someone finds this useful and I'd be happy to look into adding features if there's interest:
https://www.ebower.com/docs/ubuntu-bluray/#mkv-rename
Obviously I'd be ecstatic if Mike wanted to include this functionality in the product itself.