So this goes to something that's always bugged me about LCS.
And that's the encounter rate vs. what's going on. This is a meta issue I don't really expect resolution on, but....
Being able to track groups more effectively is what's always held back the mission simulation from being more interesting or being paced differently. When you're recruit shopping, you want tons and tons and tons of encounters, very quickly. When you're infiltrating, or have raised the alarm, you want less encounters but of a more dangerous variety. It seems like once the alarm goes up, all you see is conservatives for the most part, so its tweaking what happens at the site but only in so far as its allowed by an encounter generator.
If the game was actually playing with hard numbers of populations at a site you could do so many more interesting things with encounters. When you run into 3 sets of Police Gang Units now fleeing a site, you abstract that by thinking "Well it's just the same gang unit chasing me down" but you know that's not what's going on under the hood.
So things like, different groups of people showing up underneath tables really points to where the simulation starts to break down. If there were actual populations being generated and tracked each time you visited a site, you'd have a reason to leave a site when recruiting because you've basically tapped out the people that are there for that day and never found the ones you want. This population might be way larger than what you see in a single or multiple run of tables...but it's finite, and you'd eventually see them all and go "ok, time to go back to the apartment and come back to see who's here tomorrow."
And if you could play with the site population list during the mission (as opposed to generating it on visiting the site and that's it), it opens up a lot of possibilities for making the game world react in an even more believable way to player actions (or you could slowly add and subtract people to the encounter list turn by turn, to simulate people coming into a site, hanging out, then leaving. It's doing the same thing as we have now, but with a far higher degree of control.)