The problem is that I typically have far more battalions than I do commanders with bonuses, so I end up having to go through and assign half of them by hand afterwards. That, and the ship assignments are screwed up; some classes don't get autoassigned commanders at all, and others have absurd assignments, or don't make much sense when looked at with the ranks. So for example, I've got 4 carriers that require rear admirals or higher, 4 battlecruisers with the same, 10 heavy cruisers with commodore requirement, 12 destroyers with captain requirement, and 32 frigates + 40 FACs with commander requirement. Now suppose I've got 3 vice admirals, 7 rear admirals, 18 commodores, 34 captains, and 150 or so commanders. The autoassign will typically do something like this: 3 VAs, 5 RAs to the BCs and CVs, and then put the other 2 RAs on FACs or something stupid like that, then put 10 commodores on the CAs, and dump the other 8 into FACs and frigates, and so on down the line, rather than assigning them to the next highest command, or not assigning them at all. Half the time this ends up creating more work than it saves, especially if I want to do something like assign the officers of appropriate rank with the highest training rate to an undercrewed squadron to get them to fighting form sooner, or assign officers with very high initiative ratings to a group of skirmishers, etc.
You can set it so that they never end their tour. Its a checkbox up in the center top area if I remember correctly. Auto Assign will never take em out.
Thanks.