The first equation holds good for average acceleration, but the second is the equation for uniform acceleration. The value obtained using option 1 is correct.
In the time interval from 0 to 6 s, the acceleration changes (a constant value from 0 to 3 s and another constant value from 3 to 6 s). Then you cannot apply the uniform acceleration equation as given in option 2 directly. Find the average distance traveled from 0 to 3 s (where the acceleration is uniform) and then substitute it in the equation. Now, again do this for 3 to 6 seconds (where the acceleration is zero). Hence the average acceleration will be the average of the two calculated accelerations.
That is find $a_1$ for 0 to 3 s using the second equation (I don't know why you do this because it is already given) and then find $a_2$ for 3 to 6 s. The average acceleration will be the average of both $a_1$ and $a_2$