As someone stated above: Keep Clemenza in II and Tom in III.

Pt. I - Insert into the storyline - Bocciccio Clan, Depth of story regarding Lucy/Sonny and Back story of Filomena and Luca. (Sure, it'll make the movie about an hour longer, but what the hell--I wouldnt mind)

Pt. 2 - Have Clemenza with the family, only not in the role of Pentangeli -- Have Michael kill Fredo himself, not just giving the order.

Pt 3. - Although I think pt. 3 was just "OK", I think removing part three all together would be better. Compared to the way they made part 3, I would rather use my own imagination to find out what happened after part 2.