I don't think I really like that model. Yes, CM does get a bit clunky in how you manage the companies. (I love it when I forget to embark my company after a sustained ground war, and only realize when it their ships are half a sector away.)
But it's part of what makes the game feel like a simulation. Your suggestion would definitely streamline things, but it's less like a simulation and more like a narrow game with narrower choices (assuming you remove the ability to manually say who goes where, how.) Right now I like to have an explorator Company, that just kinda flies around the sectors, finds stuff, claims it for the Chapter and responds to nearby threats that are worth their time.
Your suggestion also can kinda tie up companies and make them unable to respond to new threats. Lots of times I'm planning go to somewhere but the situation changes. (New outbreak of something nearby I should stop before it gets any worse, ork fleeks that swell to redonk proportions by the time I've actually gotten to where I need to go, and require a rethink of where to attack and when.) If your company is just on auto pilot until they get there, you can't do anything with them. That and there's fleet management beyond just getting Astartes where they need to go. Escort ships and destroyers.
I do think there could be better ways to select companies (like if you did want to load a ship you could open the Chapter management screen and click a company header to just say "all of 'em", which takes you to the ship selection screen.) But controlling whole companies is kind of opposed by CM letting you do stuff like send half the company to one side of the sector, the other half to another and leave a scattering of wounded across half the galaxy, if you so choose to mismanage things that way. So it'd require a pretty severe rethink about what CM lets you do and not do...and a lot of that makes it seem less like a sim and more like...well like a modern game to be honest, that puts usability above granularity.
The path to heresy is often paved with good intentions and this sorta feels like it treads down it a little, toward a more expedient but less fluffy way of commanding the Astartes. I'm not saying I'm in love with the spread sheet but at least it keeps you sort of paying attention to individual troops because you have to look at them, rather than just commanding the entire company. On the other hand, when I think about it, loading guys on ships and keeping them moving around the sector is like 1/3rd of gameplay, easily. Make that super simple and suddenly you're doing a lot more, a lot quicker, which is good, but the game seems kinda shallower, which is bad.
One thing I do think would be nice: the ability to plot a course across the sector. Maybe that would be a nice compromise. When you select ships for warp transit, maybe you hold a key or toggle a check box, and then you can click a path across the sector, with the eta of each jump listed. The fleet follows this course, pausing at every planet for one turn and giving you a chance to do something. If you do nothing with them, they continue on your route. If you raid or disembark them, their course is lost and you have to replot it. Maybe the system they're shooting for has an icon or a glow or something to indicate its the destination of one of your fleets.
And since I'm on about warp travel, one fluffy thing we don't have yet is variable warp transit time, which is a BIG part of 40k lore. Right now every jump is predictable, and generally most should be. But perhaps we need an event that either lengths or shortens the duration of warp transit. (There are tales of people even arriving
before they left, but I don't think that's a sane goal to try and program.) So like, +1/-1 or more turns getting added when the event fires. Warp transit along regular warp routes should be more reliable. Traveling through the warp off the warp routes should be way more unpredictable. It kind of irritates me that Orks show zero fucks given for most warp routes. And maybe one of those global turbulent warp events should affect travel times. Maybe one of those "lost in the warp" events should make possible a "returns for the warp" event. One of the big conceits in 40k warfare is that you can't really count on people being where you need them to be, when you need them there, because of the warp, and that leads to a lot of heroic last stands and doomed last stands because not enough people have to hold out against superior forces. In order to keep it sane for players travel times should be relatively stable. But for example...
In my last game a WAAGGGH was called and I'd pretty much crushed it except at its origin, which was puking out roks and fleets like crazy. Way more than my single small fleet carrying my marines could hope to deal with. So instead of confronting them, I'd just jump to the next system over and wait until they'd crashed on the planet, then come back. It was easy to time because you know how long it will take them, and you, to move anywhere. Making those travel times a little more unpredictable would keep things more interesting and prevent people like me from gaming it so hard.
Also fleet combat is lethal as shit and almost unwinnable when it counts due to the #s involved, pls fix.