I don't believe the EMB 145 creates bad habits. I guess its all about your particular viewpoint on how YOU choose to learn......if that makes any sense. When I was new at XJT, I tried to hand fly as much as I could to really get a feel for the airplane and to get to know its quirks. It has a lot of quirks! I felt it was a great way to know how the plane was going to respond in certain situations. I'm a new capt and I'm flying with a bunch of new 500hr wonder pilots. A lot of them seem afraid of the aircraft, meaning they turn the autopilot on as soon as they can and just sit and watch it do its thing. In my opinion that will create bad habits when you're new and really low time.
As far as landing this thing smoothly and consistantly......I have close to 5,000 hours in it and I still can't figure out why every third landing feels like it fell out of the sky! Its just the way it is.