Is lowering V1/VR (and runway length required) the only reason for flaps at take off?
For an aircraft designed for cruising efficiency it is important to have as little trim drag as possible. 

See ATR 72 link:

The wing may appear unusually small, but it is made to produce the needed lift at cruising speed at its most efficient Angle of Attack, where lift to drag ratio is highest.  If the wing produced too much lift for level flight at its cruising speed, it would have to be "trimmed" to a lower AOA, at the expense of greater drag, there for a greater rate of fuel consumption.

The contribution of velocity to lift is described in the lift equation:

$$ L = \frac{1}{2} \cdot C_L \cdot \rho \cdot A \cdot V^2$$

with $L$ being the lift, $C_L$ the lift coefficient, $\rho$ the density of air, A the wing area, and $V$ the aircraft velocity.

The ATR 72 cruises at 280 knots.  In order to generate adequate lift at lower velocities it either has to dangerously increase its AOA, or increase its coefficient of lift by adding camber.

Lowering flaps add camber, which is why this plane does it, as part of its take-off procedure.
Higher flap settings are generally avoided because they produce too much drag.