All right, I see what you mean - the prison system is underused. I am not sure how to make it more used, since avoiding going to prison is generally a good idea in Liberal Crime Squad. One idea that has occurred to me is randomized story events, that might do things like add Liberals to your party but place them in prison, etc. These would be more complicated than existing events in Liberal Crime Squad, but I've seen other roguelikes (e.g. FTL: Faster than Light) that use a similar concept. The challenge comes with balancing these events with the rest of the game.
Violence is overpowered, and I've got a couple of ideas on how to fix it. My current way that I'm thinking of is that violence causes the LCS to become less popular, and LCS site actions exert a conservative influence on most views if the LCS is unpopular. Therefore, if you rely on a strategy that uses violence and nothing else, you will end up harming yourself more than helping because the LCS will become unpopular and then your site actions will exert conservative influence. However, if you can find a way to keep the LCS popular while doing violence - by publishing special editions in the Liberal Guardian, for example - then you can use site violence to improve public opinion as part of your strategy. You wait until the LCS is popular via community service and Liberal Guardian special editions, then you go on a rampage and affect other views, then go back to improving the LCS' image again.
I miss CoH. Its closure is one of the reasons why this mod exists. That said, I don't think that the LCS would have existed in Paragon City because in this game, the LCS are unabashedly the good guys, and the establishment they are fighting against are the villains. I can easily see something like the LCS existing in the Rogue Isles, and something like the LCS does exist in Praetoria, but not in Paragon. Terra Vitae could have existed in CoH (probably - there are issues there, too), but not the LCS.
The reason I haven't put genetic engineering of your Liberals to give them superpowers in this mod is because I don't feel like that is something that the LCS would or should be doing. Performing dangerous experiments on your minions to give them superpowers is something conservatives would do, not liberals. Maybe we should think about some way that the CCS could experiment to give themselves super-powers, and you could catch them in the act... Incidentally, supervillains (new endgame content) are implied to do this already, since mad science-themed supervillains exist and their minions and lairs have a mad science theme to them.