Actually, the commander problem is an issue for both battle brothers, XCOM and Battletech, because he is not really a character. He is the only character without stats and without gameplay.
XCOM 2 tried to make him special, but that fell flat.
I never had a problem with the "remote commander" concept. But then again, I really liked how Blizzard and Westwood handled the player's involvement in their RTS games.
I don't think it is a "problem" in itself, but it doesn't work too well with the idea of taking personal decisions for any of the character IMO, especially when these invole other characters you control.
Ishar also had a very thin character "friendship" system that made some characters vote for or against kicking someone from the team.
So, if you wanted to kick Thargan, Aramir would vote against it, and if you decided to assassinate him, Aramir would avenge him and kill the character you ordered to do so. So you had to order Aramir to do the assassination himself to avoid negative repercussion.
Of course, it was a simplistic system that should better not have been in the game, but it also illustrates that it can difficult to have both "character acting on their own", and player playing the characters silmultaneously.
The thing is, the reason I still remember the characters from Ishar was because of their stats and cool looks. Having 20 STR and Con (when the max was 18) on the Chaos warriors (hey Games Workshop) made them more unique than playing doll with them to me, as was having to babysit the old hag with 1 ST 1 CON that needed to be babysitted (and given tons of extra ration to make up for it).
I think X(-)COM handled it much better than Battletech by not having any character centric event at all. What made characters personality was the things they achieved (ie performing a heroic action to turn the table, or getting killed at the most inconvenient time), and not arbitrary decisions taken "out of the main gameplay loop".
I remember Sniper2 (yes, great naming, I know...) not because I let him hit on the nurse during an event, but because he was the only one to make it back alive after completing the terror mission.
King Arthur(or Crusader Kings in a way) used the event system quite differently: it was more as another way to "build" your character one way or another than to give him/her personality.
It is an old problem that already existed in party based RPGs.
In Darklands, you could play after all your initial characters had retired, but being the remote commander of a party of 4 made even less sense.
That's not a problem. You're playing all of them, there is no central character.
On that I agree: controlling all characters is better that controlling the only "non-character".