I agree about Lyon. There are really no other early war leaders that are better as AC's for the Union, until Grant comes along.
McDowell's attack rating is "2", not so good. His numerator is typically also 12 (2+5+5) because he is in the Eastern Theatre and benefits from Scott who is typically in the national capital. On the positive side, I think he trains infantry at "4", which is helpful for troops who are probably not moving anyway. Who would you replace him with?
Perhaps you're thinking of McClellan? McDowell's historical ITR is 2. Coupled with his other mediocre ratings, and a low Political rating of 1, he's always the first AC that I replace. Usually, I groom Butler for the job of TC, by giving him an Army command. Butler's high Political rating of 4, helps staunch the bleeding of PP's that the Union has each turn, and especially during the Winter of 61/62, when almost nobody seems to move, this is probably the job he can do best.
Pope has an attack of 3, but is only a two star with less than 11 command rating. The only way he could be an AC is to promote him to three star (ouch that hurts on the PP front ), and I'm not sure the promotion would even take effect immediately. You could attempt to raise Grant's command rating by having him win a battle, but that could backfire or worse yet get him killed; it will be a very long war for you without Grant.
Pope, along with a host of other middling Union generals is a poor AC, unless he can be groomed with easy victories, because of his -1 Army modifier. This, essentially turns his 3 Atk rating into a 2. Early in the war, the Union has several other commanders that similarly make decent corps commanders, but are hamstrung by the negative army modifier when they are put in a position beyond their level of competence. The same can be said of some of the otherwise excellent Confederate generals who are deadly as Corps commanders, but somewhat less so, as Army commanders.