I know on the 'Deleted Scenes' section of the DVD, we do see Genco's deathbed scene, so originally he was supposed to be in there. But throughout GF I and II we get references about what a great consigliere Genco had been for Vito, we don't really see why this was true.
I know Pentangeli was supposed to be the same character as Clemenza - but he wasn't. Castellano not playing Clemenza in GF II is as much a flaw as Duvall not playing Hagen in GF III. FFC should have just recast the roles.
They went to the trouble of showing the Tessio-Clemenza back stories in the "flashback" sequences in GFII, I always wondered why FFC didn't introduce Pentangeli at the same time (maybe as a childhood buddy of Vito's from Sicily or something, which would have explained why Pentangeli's brother was still living there in 1959), to explain why Michael is supposed to regard him 40 years later as a trusted old family friend. FFC also could have introduced a much younger Hyman Roth as being in business with Vito at the importing company - maybe running bootleg booze during Prohibition.
Still, I think GF III is much better than most people give it credit for. But obviously, it's not as good as it should have been.