Agreed on most of your points, though I haven’t seen issues with file format presets to this point. (FWIW, in case the issue may be Mac-specific, I am on Windows.)
A few additional thoughts (continuing on from your numbering in case it helps others reference the various ideas):
5 - Cut-down/alternate mixes
In my context, I’m primarily talking about full mixes (i.e. with vocals), karaoke mixes, and instrumental mixes, but it could be other sorts of cutdowns, such as acoustic, music-minus-one, etc. The idea is to have a way to specify jobs for multiple alternate mixes for export in the same queue. This would probably involve remembering solo/mute states at the time of creating a queue entry, rather than, or as an alternative to (via a checkbox preference in the job?) at the time of export.
In particular, I might want stems in my overall set of mixes, but I don’t want stems when doing cut-down/alternate mixes (since the stems would generally be the same in all cases), but I would like to have one queue operation take care of the alternate mixes, too. (The checkbox idea mentioned to indicate which queue entries are included in a batch export would be a distant second place alternative as it would at least let you exclude various operations when making an alternate mix, but there would still be the need for multiple user interventions to render the set of mixes needed.)
6 - Multiple export queues
Short of the alternate mixes possibility, another alternative might be to allow having multiple export queues, where you could choose the one you want on a specific job to run that. For example this would allow having one with stems and one without (or various other combinations, such as if you render MP3 files of a full mix but not of instrumental mixes). It could also allow having different batches while still working on a project and wanting just work mixes then different batches for a final archival run.
While this could somewhat be covered by the tick boxes for individual jobs within the queue, it would be a way of avoiding having to manually tick/untick the check boxes if you frequently run different variations on exports.
7 - Bit reduction/dithering/noise shaping options
I’m a relatively new (since 9.5) Cubase user, so perhaps there is something I’m not aware of here, coming from SONAR/Cakewalk, where dithering options are built into export presets, and you don’t have to use an explicit plugin to do things like specify Pow’r 3 dithering/noise shaping versus triangular dithering or no dithering, etc. As far as I’m aware, this has to be done in a plugin in Cubase. But if high quality algorithms are being used, it would be desirable to be able to specify this as part of the export file format presets. For example, this would allow making unmastered mixes at various bit depths with triangular dithering (if going down from the internal bit-depth) in the same queue operation as a CD quality master with noise shaping, a 24-bit/48 kHz master also with noise shaping, stems with triangular dithering, etc. As it is, because the dithering/noise shaping options have to be done in a plugin, and at least as far as I’m aware, match the bit reduction, these sorts of jobs have to be separated out into different export queues. (FWIW, I’m using PSP Audioware’s X-Dither for this since I’ve been used to it – I haven’t tried comparing to the plugin Cubase builds in. However, in Cakewalk, I just use the built-in Pow’r et all options since they make it vary convenient to store bit-reduction/dithering/noise shaping options as part of a mix preset. Unfortunately, they don’t have export queues at all.)
8 - Export queue presets???
This is more just a “thinking out loud” idea, but I’m wondering about the possibility of having cross-project export queue presets for cases where people are frequently making the same sorts of batches of files for archival and/or delivery purposes. It’s tough to say exactly what capabilities would be included here, keeping in mind that three different projects could have three extremely different sets of tracks, buses, and routing. I’m assuming whatever would get implemented in export queue enhancements could be set up at a project template level, which could cover some of this general thought, but I’m more looking at the case where every mix is different, yet there is a relatively common need for deliverables, such as:
- 24-bit/48 kHz stems
- CD quality full mix/karaoke mix/instrumental master
- 24-bit/48 kHz full and instrumental masters
- 24-bit/96 kHz full and instrumental masters
- unmastered full/karaoke/instrumental mixes at 24-bit/96 kHz and 32-bit 96 kHz
- full MP3 mixes at various bandwidths
or whatever an individual’s specific commonalities might be. A big challenge would be deciding what is included in any given definition (e.g. stems, karaoke mix, instrumental mix, acoustic mix, etc.) in a general sense, but maybe there could be some capability to specify that within a given project similar to how things are now checked when picking what appears in a single job, but, in this case, making those selections based on a job preset definition (e.g. for bit-depth, sample rate, format, “type of job” name), rather than starting from the list of tracks and creating a job. Whereas others elements might never change from project to project (e.g. various bit-depths/etc. from the Stereo Out as a full mix).
The idea (when combined with the various other ideas in this thread) is really just to make a quick way of doing a (potential one-time) adjustment in each new project to define what gets included in any queue job definitions that need clarification for the specifics of a project. If users used consistent bus naming, some areas might not even need changes across projects with very different tracks. (For example, for a karaoke mix definition, if the users were using an Instrumental Submix bus and a BGV submix bus in all projects, the definition might just involve including those two buses and to include processing through the stereo out.)
Okay, I won’t be expecting this feature in the first patch of Cubase 11. 
Rick