[Fyron]

You could use SJ's active CI system. There are no stock CI projects. Instead, CI consists entirely of intelligence sabotage projects. This way, not all projects will be blocked by a magic wall and intelligence actually becomes part of the game. Expensive projects become harder to pull off, not easier. There are more chances of them being hit by an active CI project (it is in the queue for more turns), unlike the stock system, where cost is the key factor in how hard it is to defend against that project. This system will not work so well with AIs, since we have no influence over their selection of intelligence projects. An AI trait that gives the AI some standard CI projects might help them out. But for human players, it works great.

About leaky armor and randomness... You can reduce the randomness by increasing the hit points of the armor components. Randomness is definitely a major purpose of the system, however.