The big C&C will break down to what happens to the following, with my guess at the sort of options you have in parentheses. I'm obviously less certain about these things than the big picture stuff.
1) Johnny Silverhand and your relationship with him (destroy/betray him, assume his memories or whatever, give him some sort of peace, enact his revenge, reunite him with his girlfriend, in some combination)
2) The Walled Off Internet and Alt Cunningham (moar viruses, corporate control, restoration in no one's hands)
3) Who rules specific parts of Night City and what happens to them? Outcome of a possible Militech-Arasaka corporate war? Which particular members of each of the corporations ends up ruling.
Hopefully there is more. V's fate could go a lot of ways too, and I'm hoping less obvious choices have repercussions down the line, but that's probably pretty doubtful outside of cosmetic differences.