You can put on financial constrains, lowering the mone you get, or make wages higher etc..
Make a proper research tree, demand live Alien cptures and so on... lot's of possibilities.
If you like you like you can give my Mod a try, it should be way harder then vanilla.
I hope you can accept failing missions
You can find it on the Modportal
hereSorry for the shameless selfpromotion.