This may already have been said...but if not then I have a solution, at least for Monarchies: a regent (or his/her consort?). If the issue is mechanistic. and the worry is what to do (game wise) when the King is in command and thus not ruling, then a regent is the natural choice for a mechanical remedy. When the King is going on campaign at the head of his army, he should have a regent in place who rules from the capitol in his stead. You can designate someone for this task beforehand. Of course...there could always be a risk that things happen while the King is away. Maybe the regent is an incompetent fool. Maybe he is a treacherous rat who tries to take over. All of that can be part of the risk of putting the King in charge of a military force.
Now I know the situation will be a bit different for Rome, with two consuls, but as I understand it perhaps that can be the solution. Since the 2nd consul acts primarily as a stat booster for the primary one (like the royal consorts), if the first is out on campaign maybe the 2nd takes primary charge until the primary returns from the conflict. Of course, this would have the potential for more political intrigues. The consul already heads the levies of Latium when they are raised. So if the other issue is who should command them, then perhaps a chosen general can be put in place temporarily to lead them (should the primary Consul be leading a legion instead). Interestingly...the Co-Consul CAN lead fleets on his own while in office....
Altogether though...I can see the mechanistic concerns from PDXs standpoint. Rome won't get actual, standing legions in the game until the Marian Reforms law is passed, as it was in reality, so having consuls be able to potentially lead them shouldn't be a big deal until later in the game anyway. In the previous hundreds of years of Roman history prior to Marius, they just raised and fielded ad-hoc legions of levied troops as needed. This doesn't mean that they were all "peasants" however. I think some players need to get the medieval sentiments from CK2 and CK3 out of their head. In the Ancient World, and particularly where Rome was concerned, levy does not equal BAD. Your levies aren't just illiterate peasants with pitchforks who suck and act as cannon fodder.
The ranks of the Roman Army, from the early slingers and skirmishing troops, right on up to the Triarii and Equites were all "levies" - as in they didn't remain organized and as a standing force AFTER a particular war had ended. All of the troops, of both high and low quality, were levied temporarily. Now here, in this game, governors lead the outlying regions' levies, and their potential to act disloyally is a big part of the game's intrigue. So they should NOT be able to command your field legions. In the same way, the Consul leads the capitol province levies, as I said above. So really what the game is driving at mechanistically is for the generals granted command of a permanent, professional, standing legion who AREN'T office holders, to be able to accumulate political power on their own via their legions. This is in the vein of Marius, Sulla, Pompey, Caesar, etc. None were consuls when leading their forces (I think). The goal of the legions in the game is to act as both military forces, obviously, but also as vehicles of political intrigue for men like these.
In that sense, I don't blame PDX for walling off generalship of them from national leaders. This is because these people ALREADY have power. They are already in charge. The "consular legions" of old whom the two co-consuls themselves took on campaigns against the Samnites, Carthaginians, Macedonians, etc, are already moddled by having the consul lead the capitol levies. As I explained, they weren't standing forces. If we truly tried to model an accurate Roman military-political structure in this game, it would be...difficult. Consuls only had ONE YEAR terms; that's why it says at the top "In the Year of the X and Y" or what have you (the two consuls' names). Obviously however, for the game's sake, five years is what is easy to deal with. Otherwise, you'd be constantly bombarded 24/7 in every in-game year with political intrigue. If the events had the same rate of firing as they do now with five year terms, whole Senates would come and go and many years of administration would role by with hardly a notice and no intrigue or events. You would have nothing or you'd be driven insane. PLUS - you would need WAY MORE CHARACTERS to faithfully do this one-year turnover, especially given the ten year prohibition on the re-election of consuls. So in conclusion, I get why having national leaders lead the game legions could be very tricky...and I don't see it as a huge issue. But, perhaps looking at the Consorts, Co-Consuls, or some other kind of regent could offer a reasonable solution for both camps.