I can't claim to be able to compose an exhaustive list, but a few issues come to mind. I would also preface by saying these are not necessarily reasons to criticize Foote specifically just some facets of the evolution in thought concerning the war.

The gradual decline of the Lost Cause mentality has led to a reexamination of the merits of many generals, and to a lesser extant politicians. For example the reputation of James Longstreet was largely restored following decades of being blamed for the Confederate defeat at Gettysburg. Historian Glenn Tucker began examining and disputing the writings of Longstreet's critics in the 1960s. The shift in interpretation has also been attributed to Longstreet's favorable portrayal in the popular novel The Killer Angels by Jeff Shaara, published in 1974, the same year as Foote's final volume. Increased recognition (it won a Pulitzer) and more academic treatments followed.

There has been an increase in the amount of attention devoted to the Western Theater of war, evidenced by such works as Peter Cozzen's trilogy *The Civil War in the West: From Stones River to Chattanooga," published 1990-4 to his 2006 book on Iuka and Corinth. Consequently, the west is considered more important than it had been previously. (There is a great line about this in BCoF, but I stupidly lent my copy to my brother.)

The analysis of the Civil War as "total war" has also been called into question, such as in Mark Grimsley's The Hard Hand of War and Noah Andre's Southern Storm. "Hard war" has been used by some as a replacement to indicate a strategy focusing more on property than people and to somewhat relieve Sherman of his portrayal as an evil pyromaniac. On a related note, the analysis of irregular warfare and partisan rangers like Forrest, Mosby, and Morgan has been wider and harsher, for example in Robert R. Mackey's 2005 The Uncivil War.

All that said, the most common criticisms of Foote I have seen are his failure to clearly cite his sources and, that, as James McPherson said in his AMA, Foote "never met an anecdote he didn't like".