My only real issue with Evil Genius was that the "front" you put up never worked. Enemy agents would come in, immediately zero in on the route to your base and just start trashing shit left and right. Traps, decoys, all that nonsense was a waste of time. It was far better to have an empty parlor up front, a long corridor for them wander down, then you just dog pile them with a big trap room. I got so sick of having to constantly rebuild everything they trashed I eventually gave up.
Something I did that did delay the agents a lot was building hotels with a ton of 1x1 rooms with doors on all sides. They'd waste a lot of time shooting the doors. But yeah that was tedious to replace. Putting big blocks of machine gun nests outside ended up being less hassle, backed with security cameras so that guards would swarm into the location. Deal with it like an RTS defense situation, and drop the pretense.
Also, building your barracks or troops training areas in the entrances can help too. Same thing as works well in Dungeon Keeper. It's faster to replace minions than equipment.
It worked up until an agent goes hostile and starts a rumble that nukes your social minions. Then your regular minions get mixed in while they tried to clean up, then your guards when they are sent in to guard your clean up crew.
Well there's something that could be fixed there. The intent was clearly to emulate James Bond movies, so they failed because at any point the designers should ask "what would James Bond do?" do in this situation. James Bond never went around machine-gunning down every waiter and waitress in sight.
One fix would be to make it so that enemy agents only shoot your armed minions, but will incapacitate unarmed ones. Another possibly simpler fix would be to make it so hotel staff are a type of civilian that arrive on the island automatically as needed the same as the tourists. Then hotel staff wouldn't be aware of the secret front, and they'd freak out if a shootout started or they come across something they're not suppose to see, and need to be brainwashed and released again so as not to spill the beans. You'd probably still want some social minions but make them more iconic types: But the point should be that if their cover is blown, these minions whip out weapons and have a shootout with the agents. "good" agents should never gun down unarmed people.
The core problem here is the simplistic enemy agent AI that defaults to treating the game as an RTS.