What I said in my previous post was slightly wrong. The time you calculated is only approximately equal to the downward flight time. (I was thrown off by you saying you found t=2.00 s. Using your numbers and formula, you actually get t=2.15 s, not t=2.00 s.) The reason for this is because your numbers aren't consistent with the actual flight of the stone. When the stone's downward speed is 19.6 m/s, the same as its initial upward speed, it's only fallen back to its original height, which is 1.5 m above the ground, so it's actually only fallen 19.6 m, not 21.1 m. So the numbers you're plugging into the equations aren't consistent with the stone's flight.
Physics texts are often kind of loose with the notation, which can unfortunately lead to misconceptions. The equation you used should actually say
x-x_0 = \frac{1}{2}(v+v_0)t
The pairs x, v and x0, v0 need to match up. In other words, when the stone's displacement is x0 or x, its speed is, respectively, v0 or v. In this problem, when the stone has fallen 21.1 m from the apex, it's moving faster than 19.6 m/s, so you can't plug in the pair x=21.1 m and v=19.6 m/s and get the correct answer.
So getting back to your original questions, the main reason the equation you used isn't particularly helpful is that you don't know the final speed v of the stone right when it hits the ground. On the other hand, you do have all the quantities needed to use the equation the book used. Also, your approach only gives you part of the time of flight (if you had the correct final speed v). You'd still have to do another calculation to find the total flight time. There's nothing wrong, per se, with doing it this way, but it's unnecessary to break the trajectory up this way. It usually just makes the calculations more complicated.
Also note that the x that appears in the equations isn't distance; it's the displacement. Similarly, v isn't the speed, but the velocity. These are vector quantities. If you're consistent with the signs, your calculations will work out without resorting to breaking the trajectory up into different pieces.