It's basically two interlocking problems resulting from that March decision about corps, yes. It locked in commanders and they weren't very good ones, because the decisions had to be made before they'd been tested (and then you couldn't get rid of **** ones).
There is at least one case of an army subdivided into more than 3-4 corps, though, Sherman's army outside Atlanta. My count is:
4th Corps
14th Corps
20th Corps
15th Corps
16th Corps
17th Corps
23rd Corps
(plus a cavalry corps)
Sure, these are divided formally into three different armies, but that doesn't alleviate the problem except insofar as you could consider the armies to be basically the wing command level (though they're lopsided if so). But for a lot of the campaign there's the same basic problem that the Army of the Potomac had which is that there's seven distinct corps and they add up to less than 100,000 men, meaning that the corps aren't much bigger than divisions should be.
You could also consider Lee's army outside Richmond to be this from the other direction, which is that several of the "divisions" are actually as big as the Union corps they're facing. The Army of the Valley (Jackson's command) is basically a fairly bulky nine-brigade ~45-regiment corps, but then the rest of the army includes:
DH Hill's division (5 brigades, 23 regiments)
Magruder's Command (6 brigades, 28 regiments)
Longstreet's division (6 brigades, ~25 regiments)
Huger's division (5 brigades, 27 regiments)
AP Hill's division (6 brigades, ~28 regiments)
And the Dept. of NC, which is a rump command with about six regiments.
If these were Union formations they'd be called Jackson's Corps, DH Hill's Corps, Magruder's Corps, Longstreet's Corps, Huger's Corps and AP Hill's Corps. The force is big enough to justify at least four corps though.
There's also an argument to be made that a lot of the corps which are formed (by the Union, but not just by them) during the war don't really fit how corps should work. The ideal for a corps is that it's a self-contained miniature army, which means having multiple subordinate infantry formations with integrated artillery (i.e. divisions) plus at least some cavalry at all times so it can perform scouting duties for itself.
The maximum size is about 30,000, maybe a bit more, while the minimum size is a bit harder to define (as it depends on doctrine). British corps in 1862 were formed of two binary divisions and a cavalry brigade, so it's not very big (about 12,000 men all up) but these corps are definitely fully independent manoeuvre elements in their own right. I can definitely see an argument that if you have a single army of about 30,000 men it might be good to split it in half to provide independent manoeuvre elements, but equally you could just use the divisions in that way.
If I had unlimited latitude to reorg the Union army after Second Bull Run, I think what might work best is to basically take the strongest divisions without regard for corps org, brigade new regiments with old (to bring up the strengths accordingly, but definitely interleave them at the brigade level) and form four corps of about 25,000 men each in three divisions. Attach one cavalry regiment per corps and consolidate all the rest into a cavalry division, with the cavalry division basically being "the cavalry which can act independently"
The point here is that you want to have forces able to be manoeuvred without needing to constantly think about having to support one with another.