I see a lot of people mentioning "bad habits" but nobody saying what they are.
Could you elaborate on that?
Using a simulator doesn’t let you build that feel, so you end up spending a lot of time looking at the instruments. When you step into a real plane that can make things difficult, as you’re supposed to be able to maintain altitude by just looking outside, etc.
Essentially, if the problem is that the instruments are used as a crutch, isn't it "just" a matter of taking the cructch away for a while?
No can do.
Because whilst during training you should be spending 95% of your time looking out the window, the remaining 5% are spent bashing it into your head how to do an effective instrument scan and also there are parts of training where instruments get combined with the outside environment (such as learning to get a radio fix if you're lost and correlating that with what you see out the window).
Obscuring instruments is sometimes done, but that's much, much, later down the training line.
You can't even "feel" the plane in FAA-certified simulators, so I'm not sure how you'd feel it on a laptop with a joystick and plastic rudders. And of course the big issue - if you're VFR you need to be looking for traffic because nobody is handling separation for you except you.