As a primary MVAM pilot myself, this would be nice, but I would consider this very low priority.
I rotate through the different configurations that I fly when I engage MVAM mode, and there usually isn't a problem with me having to wait for cooldowns when I first enter an instance. I do try to use MVAM when appropriate though - which isn't necessarily all the time, the simpler battles I just stay integrated.
From a coding perspective, non combat pets, and MVAM in sector space are completely different, and would require new tech to allow the use of MVAM/Saucer Separation/related abilities in it. (Well, that's a guess, but an educated one, and I'm 99% certain I'm right on that.)
Similarly, saving the state between map transitions would, while not impossible, be more work than you might think, since other factors such as the shields/heatlh, torpedo cooldowns, destroyed state etc. of your other parts need to be considered (and my loading screens take long enough as it is!)
Also, the timer on it gives the use of MVAM some strategy, if it persisted between map transitions, using it would be a no brainer, with people only reintegrating when parts get destroyed, just to get a new one, or maybe pilot a different section. With the 2 parts you aren't currently using starting cooldowns when you first initiate MVAM, I find that if I really want to split up after dying, or a map transition, I can just fly a different section.
While I agree that persistent MVAM state between changing instances and the like is extremely low priority to the point of being unnecessary for me...
I however do feel extremely strongly that the MVAM abilities themselves need to have their cool-downs radically lowered, to a fraction of their current time. As it stands, separation during battle that would necessitate or benefit from it is neigh suicidal because of course you basically park while blooping around for the agonizing time it takes to actually separate.
Separation basically needs forethought, as of course separating after the battle that would make use of it is sort of like closing the barn after the horse has already run out...
As such, relegating the MVAM to near irrelevance as a result of hardly being able to make use of it due to the preposterously long cool down(s) effectively removes the entire point of separating since you quite often can't do it...
I am also a MVAM user, and the stand still to me is also very minor and if your tactical about it,even useful really.
Often I come in assembled together, fire off Cannon Rapid fire and Tachyon beam, once I about to need to turn my attack run to one side or the other I then hit the mode I want. I come to complete stop giving me more time on that shield and then once I start moving the pet keep hitting it while I spin around. BOOM KOed with only one shield side hit.
Also on NPC that use evasive maneuvers, trigger it right then, your pets usually branch off in two different directions thus again even with the speed bonus the NPC takes your still hitting the side you wanted.
So in my personal opinion, would the requested but nice.. sure I will NOT complain about it, But I do have to agree very low on my priority list.
That can be annoying sure, as well as the fact that I always seem to outrun my pets while at full impulse by a fair margin. I'm not sure if it is a bug or not, but at times when this happens they stop following. I backtrack and they are just sitting there.
Quite a few times one or both were brilliant and stayed near an exploding ship and get themselves disabled. Not the brightest of pets.
Truly. I love my MVAM, or rather that module placed in my original Prometheus class, but the pet management is pretty poor.
I'd rather see the AI on them and the following speeds fixed before the cooldowns though. As others have mentioned, once you take out one target they follow pretty lethargically and often just stop in the middle of the map while you're at full impulse.
I don't mind a cool down on them, but the way its handled is a bit poor.