I would lose the class based and make it skill based, you have all 3 skills in a basic form and need to practice each one and get better at themand have each mission have multiple ways to do it but only 1 would be the best method and that could be use all 3 at different times. stealth into the compound, switch to conman to setup a clear extraction route and pass the guards at the target itself. once the target has been aquired set off a distraction that was setup in sneak mode like a smalll explosive on a window to set off a security alarm or a device that sets off the fire alarms. then once the distraction is happening use spy to blend in and walk right out the main door. other missions could be acomplished with just one skill such as stealth to the roof and rope down to a window where the target is at, grab the target and stealth back out, you could try to spy or con your way in but the guards are more alert. Another could be the location is too well lit, and theres only 1 way to get to the target and it requires you to con the guard.
Then you need to have a variety of missions, always thieving would be boring so maybe some espionagewhere you are hired to get the layout of a location, guard routes and schedules, and where a specific item is located without being detected. then you have the basic theft job where you go in and steal something up to complicated by having to access several parts of the compound to gather multiple items, such as a prototype piece of tech, the software used in it from another lab, and the design schematics from another. The last mission type I can think of is planting something instead of removing. Examples could be a trojan virus on the secure system, planting false evidence, or changing some research making them start following the wrong research path. and missions could be a mix of the main types like both stealing research and planting false. doing recon and stealing keys. or recon, stealing something, and planting false evidence in its place.