www.makemkv.com

Would appreciate if there was an option to enable all subfiles by default instead of activating all audio streams and subtitles manually for every single title.

Have you looked at using Expert mode, and changing the default selection rules?

My settings have everything except 3D MVC being selected automatically...

Yes, found it. Changed default to "+sel:all".
For German users: This helps to find out the meaning of the configuration: https://wiki.ubuntuusers.de/MakeMKV/
@developers: Why not show the advanced tab straight away instead of opening it by expert mode?

I cannot speak for Mike on why various things are tagged as "advanced", but there are good reasons to not enable expert mode automatically... There are a lot of things in the advanced section that can make MakeMKV "malfunction" if you don't know what you're changing.

A good example is the selection rule - it is sensitive to other settings, like "preferred language".

But you need expert mode to use profiles. And profiles contain their own selection rules, which override the default rule. It can quickly become a problem if you don't know what you're doing.

Maybe there needs to be an "intermediate user" mode...