In decreasing order of importance for me would be:
1) A rework of endings. And I mean a rework. Or additional endings, or continuation of several existing ones. Basically, endings that aren't "you lose". A proper "you succeeded and won, you beat the impossible odds" ending. Maybe raiding the crystal palace. Maybe going after Biotechnica cloning tech (Aldecaldos have Biotechnica contacts, after all). Hell, Misty cranking out real magic to save V - work out a deal with Shadowrun owners or something and heal V through literal magic. That would be a twist.
2) Expansion of existing in-game content, and specifically character interaction. Both in terms of quests and non-quest interactions. Most of all I want V, especially street kid V, to interact with her family. And yes, she has one. Mama Welles, VIctor, MIsty. People who clearly care for her well being beyond "professional self-interest". Have V secure Victor new supply routes for cybernetics. Console Misty long term over Jackie's death, serve drinks at El Coyote Kujo while the normal bartender is unavailable or get Mama Welles out of the City altogether.
I also want ways to deepen inter-character interactions, where all interactions aren't just V-NPC, but can lead to NPC-NPC interactions. Introduce Judy to Kerry Eurodyne as a clearly supremely talented BD artist, and see as he sponsors her first "Mass media" release (especially if it's the underwater exploration one), and see later how she is flirting with Red Menace if you aren't romancing her. Give Victor's data to River so he can get new implants reliably to see him sporting new cyberware and investigating Gary's disappearance (which was a kidnapping) later. Then use River's old police contacts and / or your new buddy the Mayor to smooth Aldecaldo's interactions with the city. Warn Regina about Lizzy Wizzy's oncoming cyberpsychosis in time for it to be prevented. Stuff like that.
And make those choices matter, dammit! See how they change people's lives. Meet Judy in Aldecaldo's camp if she decides to leave the city or staying at Kerry's / Denny's if she makes it big in BDs. See Misty going out with River. Etc, etc.
Ideally you'd do this with stuff like Gigs and Police activities too. Like, getting some sort of cred with police, so if you finished like a hundred police activities, River would know you from the start, and you'll get additional options with the police, including maybe access to some of their intelligence. Or if you finished all of Wakako's gigs, you get some sort of pull with Tyger Claws and can use it during the Clouds storyline.
3) A rework of cybernetics. I am sorry, but right now cybernetics are just so much slag. Most of them give numerical bonuses to stats and that's all. And the "implants are incredibly invasive procedures that require time to recuperate" lore runs directly in opposition of how in less then a month you could go from barely chromed kid to essentially a full conversion borg and still have time to do all those missions.
Make cybernetics visible - if you swap out you entire ribcage and install a second heart in a backalley clinic, you need to have at least some signs of the procedure having being done. Make cybernetics have more qualitatively unique effects, like night vision, invisibility, echolocation, slow motion, poison gas release, etc. Make the procedure of getting cybernetic lore friendly. Like, explain how V became essentially a barebones full conversion borg prior to the second act, so she could plausibly switch implants quickly in game time during it. There could be a whole story there, in that half a year time.
Add animations for cybernetic installations.
4) Make gangs actually meaningful and present in the game. Ideally stuff like gang warfare activities, which you could interfere with and influence. Maybe push Tyger Claws out of Megabuilding H8 (I think the number was) before Clouds events, which will open new paths there. Definitely expands Mox through Judy.
5) If the technology allows, make it so you could actually start assembling some sort of team. The woman you saved with Jackie could be your net runner, Panam or Mitch or some of the Aldecaldos as you second gun. Basically, V was supposed to operate together with Jackie and T-bug. She wasn't a solo operative. Make it so she could reassemble some sort of team.
And, tied to that, expand on the half a year period with Jackie. Definitely do that. It plays well with cred system, and half of gigs could be shoved there. Add quests with Jackie and T-bug to promote bonding with them.