I don't believe that Albert Sidney Johnston was over-rated at all; I don't necessarily know that there was enough information out there to actually rate him all that much, but I do believe that the politics of the day dictated that the sites for both Forts Henry and Donelson were both poorly done. The ideal spots were in Kentucky, however, Kentucky being a border State, it was determined to try to allow the Union to make the first move into Kentucky, and therefore both Henry and Donelson were sited about as far north in Tennessee as possible.
Unfortunately the best site around Dover, also required that Henry be sited in a particularly bad spot; in fact had Henry *not* surrendered when it did, it was going to be flooded out; which is a real tough one to call any general as being responsible for.
Also, too, Foote does a pretty decent job of spelling out the strategic situation facing Mr Johnston in the west - an impossibly long frontier with some particularly crappy defensive sites that pretty much meant it was going to be impossible to defend. With Kentucky trying to walk the tightrope of being a border State, it meant that the obvious and actually only available defensive line of the Ohio River was not available to the CSA.
Johnston's loss at Shiloh was much more about trying to attack in column in the woods than it was anything else - however it was also similar to what Manstein actually pulled off at Kharkov in 1943... when the Soviets were overextended. The timing of the attack was both an opportunity for Johnston as well as forced upon him -due to the fact that Grant and Buell were about to join. Both Union armies had the Tennessee River between them. What had to be done, had to be done before Buell arrived.
I don't think either, that it should be discounted, that at the time it occured Pittsburg Landing was the largest battle of the war, and no Southern commander had ever commanded an army of that size in battle to that date.
Since Johnston died at the battle -if he has a fault, it is not understanding that he was in fact bleeding to death and not scratched.
Incidentally, the Daughters of the Confederacy running Beauviour down there in Gulfport Mississippi had a museum there where they claim to have the minie ball that killed A S Johnston.... considering the fact that I don't think they dug a bullet out of Johnston --- it seems a little improbable --- like one of those medieval religious relics...

I don't think Sherman was overrated either ... in his March to Savannah he basically disappeared completely from everyone including Washington - it was an incredible gamble, considering there was no actual line of supplies nor any ability to supply to come from any conventional sources; and they attracted a large amount of refugees.... so nothing was really a given. His Atlanta campaign proved that maneuver wins campaigns -which according to Liddell-Hart is really all that matters.
Who was? Good question ... while guys like Butler were awful, I don't think that they were largely rated as anything more than awful -so let's see... go with a pathologicaly narcisstic guy...
The Pathfinder (Fremont) seems to fit the over-rated bill... although he was apparently ahead of his time in wanting to whip out a form of emancipation into the war strategy mix.
I think Winfield Scott was the most under-rated - it was he that first came up with the Anaconda Plan -which is what ultimately went a long way towards the end result. Never mind that McClellan did all he could to get rid of the old soldier.