Full simulation of a micro controller should never be expected. Real world testing is required. To rely on the simulator to do all this work for you, puts your pocket book in their hands, and takes your understanding of what's going on out of your hands. You could spend less on the test equipment to let you figure out what's going on yourself than you would on the software that simulates it, and will not accurately represent your real world circuit in the end, only your real world circuit does.
For the cost of even the more basic single user licenses of Proteus you could by a logic analyzer and a scope.
For the Platinum edition you could outfit an entire lab with gear and components, and likely still have enough left over to buy a used car.