www.makemkv.com

1. Single file
It would be nice to be able to output a single merged MKV file of
all episodes on a disc. I've checked after reading here about source file
names and every one I've got on BD disc has episodes numbered 70-76.mpls
which gives the correct sequence every time.
When merging strip the episodes to a single language/subtitle to match the streams
This would save a whole merging sequence of maybe 45GB each disc..

Deleted Episodes or other files seem to be numbered 200.mpls upwards
These could be saved seperately to be checked - save with .check filename maybe?)

2. Audio AC3
I cant get it to output audio as AC3 - this would be really good.
(Can it do this already - I see there is a conversion option)

3. Empty subtitles
Leave empty subtitles in the output MKV for outputting single episodes
as later merging requires the same number of streams or it doesnt merge.

PS thanks for a very useful program.

You are really describing the characteristics of a single series; it's not a generic layout used across the industry. Even within a series, it can vary.

"Empty subtitle tracks" are only deleted if they were being created by MakeMKV (pulling "forced subtitles" from a regular subtitle track), not if they're present in the actual BD play list.