It's my opinion that despite the rather straight edged nature of Tom's character FFC and MP perhaps added this edge in to show that Tom is indeed not as straight or as good as he originally comes off as. GF I tended to romanticize the life and painted things in black or white.
The irony of Tom and Vito in the first film is that although they are criminals of the highest sort, they never really do anything that we can disapprove of. Vito's rationalization that prostitution, union control and gambling are victimless crimes is delivered so elequently we beleive it very readily.
Another insight, as I feel it is, as elluded to in the film (GF II). Michael mentions that it's harder to be stronger for the family because times are changing, implying that things are no longer as black and white as they were before, not as cut and dry perhaps; more complicated. Tom having a mistress by no means paints his character in black or white, it puts his character in the gray if anything. Even Vito is in GF II is a murderer and a theif (albiet a noble one) who if you take in the deleted scenes committed 4 murders and stole numerous goods.
Much of the first movie's resolution dealt with a sense of justice being proportioned to the 5 heads, Tessio and Carlo. However, I feel the second movie deals more with gray issues, like the death of Fredo, the seperation of the immediate family due to the very act of keeping the "family" in line and on top of this rat race. Much of what goes on in the 2nd movie is not black or white, cut or dry and this dimension along with the Tom dimension adds much to emotion of the second film I feel.