I imagine if Philly wanted to drag it out a bit, Chandra could have easily been flipped into full LI. She had a significant presence, but never enough to impact the story so hard that fleshing her out would have caused a disruption in the story. Every ending has Chandra left in the perfect spot for MC to stand at her side. It's so easy that it makes you wonder if that wasn't planned at some point then scrapped.
Shanlon also had a big presence, but her character's actions were so crucial to the overall story and incompatible with a romance ending. Venus would have been a fun sort of joke ending that wouldn't have required a lot of writing. She was also left wide open.
You might be on to something, thinking back on it, I can definitely see where Chandra would've been a full LI and I agree that it does feel like it was an initial plan that fell apart. If I had to hazard a guess, she might've been an initial and important vector to get to her mother and had a full LI route planned out, but it ended up pivoting for some reason.
Shanlon definitely felt like she was designed to be the wild card, it feels like her place was set in stone from the beginning since she's, as you said, very crucial to the story.
Venus I feel was a slightly misused potential LI that could've taken a real Blade Runner twist, especially given that she was slowly turning more and more human in her behaviour. I honestly wish there was more exploration along those lines as it would fit so well into the overall future dystopian feel, it would be a pretty nice nod to a great piece of fiction AND be fairly novel within the AVN world.
I still wonder as to why the dev decided to give Venus that twist, it feels more intentional than for her to just be a supporting character.