Positioning of the engine can severely affect the aircraft's CoP and CoG, having it directly at wing level must move CoP or CoG in abrupt ways.
Also, if an aircraft engine were to be creating fluctuations of exhaust gas, then the lift of the aircraft will also fluctuate.
Throttle of the engine would not only affect how much thrust the aircraft produces, but also how much lift it is using. If you wanted the aircraft to go faster but not gain any altitude, you would now need to pitch the aircraft's nose further down since a high amount of exhaust gas is being blown into the wings that is essentially adding to the aircraft's relative airflow and (if any) headwind. If a lot of lift is being produced, that is beyond the maximum deflection of the elevator, you may have some trouble maintaining altitude. To combat this, you could use flaps and spoilers, but these shouldn't be used at high airpseed in the first place.
The pilot also has to account for more factors. He/she must now also account for the additional lift that the aircraft's exhaust is providing for the aircraft.