The data disc is probably the worst thing in LCS per investment and payoff, considering that the issues can be swifted substantially with even less epic Liberals. I'm in for implementing cool new variety wherever possible, and data disc is certainly something that can be enhanced with such variety.
Also, tbe CCS. They aren't exactly challenging (at least to someone who's played for years) unless, of course, the player encounters one of those bad dice moments and gets caught with their pants down, just about to say "Oh crap, I sure hope the CCS won't become active now". Dealing with the CCS, if the player is even slightly prepared, is a matter of repeating a task that's quite trivial - sitting in a CCS safehouse and killing people. Very little thinking involved, but there is always the risk of losing a squad member to a failed datenap (arguably good, as many games are about handling risks)! Jon is working on improving the CCS infiltration system, and I'm very much looking forward to it. Pperhaps the CCS itself could be enrichened, like them having safehouses for different purposes. Destroying their armories would make them rely on revolvers and shotguns instead of M4 and AK47. Destroying their conference rooms would severely reduce their political impact. Destroying their barracks would prevent (or weaken) their raids and reduce their numbers. Something like that.
I'd also strive for making each site look unique and pretty, even if it means sacrificing some of the maps' randomness. Current maps are next to useless anyway, unless used well - the typical armed raid will only need one room to kill people in and then get out. Each site should have unique flavor options mainly (but not exclusively) aimed for stealth Liberals, similar to the Cable Studio and industry machines, but I think they should be greater in number, even in sites that already have such stuff. Stealth burglars should be favored because the current stealth method for damaging a site is spraypainting over it, which is rather... meh. However, having actions that work with less stealthy military squads as well would add incentive to move away from the exit and actually risk something. And, as for purely flavourish changes, I would like some aesthetic additions (coloured walls, carpets, smoothed pillars, more wall texts, fountains and more!) to add a means for setting a clear visual tone for each site. Factories could have brown walls with visual dirt on them and so on.
At this point, I re-read my entire post, fixed most of the typos I spotted and decided to go to bed. Nite.