Bit of minor spoilers here, not something big, but still...to have sidequests affect the whole thing organically and accumulatively instead of in a binary way.
Not true, still binary to some extent. At the start of the last quest you can choose between 4 options. 2 of these are unlocked by the completion of 2 character's sidequests prior to the events of this last quest (a point of no return, by the way).
Now, if you:
• Do Rogue's sidequests: you can choose to have an ending with her,
being a part of the major leagues
and her Nomad clan
Takemura's (Arasaka) path or suicide
Big spoilers now:
• Last quest on Rogue's or Panam's path:
After you jack into Mikoshi, you can choose between getting your body back (the endings I mentioned) or entering Cyberspace (Temperance).