I believe The Beatles: Rock Band came the closest to being perfect. Eveything about that game was just beautifully done and the only things missing was Pro Drums, an option for Keys, and a few more Beatle songs (Hey Jude, Strawberry Fields Forever, Yesterday etc. etc.)
I felt they needed a more elegant way to balance control vs chaos. The fact that you are able to pause and issue orders means that to get the best results, you should always pause the instant something needs to change and issue orders. At which point, it probably could just be turn-based, but then you entirely lose (rather than, as I think it currently is, mostly lose) the sense of urgency and chaos of everything going wrong everywhere at once and having to chase around fixing problems.
I think what they actually needed was a middle ground of a pause mechanic. Set it up such that you only have a finite ability to pause and issue orders so that most of the time you are best off issuing them live but you can also pause to issue orders where it’s most critical to do so.
The simplest implementation I can think of to try for that is to literally just have a pause meter. Either every time it fills up that allows you to pause to issue orders once (at a time of your choice) or have it be one that drains whilst issuing orders paused. (You could still offer a regular pause option that just doesn’t let you input orders. It would also open up the possibility of different ships, races, damage, sabotage and upgrades effecting your paused orders resource.
I think if they’d nailed that element then for me it would be a perfect game.
FTL has mod support IIRC. That would not be one I would use, but I bet it would have an audience!