My runes for ap cho are flat ap quints, Magic pen reds, mana regen yellows, and scaling MR blues.
Thunderlords is easily the best mastery for cho.
For the boot upgrade, I really think distortion is the the best, especially now, where you can get a 180 sec cooldown flash. Flash is super important for ap cho, because he needs a way to get in melee range of priority targets and he doesn't have the tankiness will a full ap build to get to the backline and not get kited or bursted down.
And now for why I don't build RoA...
RoA is a really strong item for cho, but it also decreases your kill potential in lane, since you have to put 1200 gold into an item that offers no offensive stats. With RoA, you have to wait for late game to reach your full potential, and also, you won't be able to reach full cooldown reduction with RoA.
With morellos first item, you have the raw burst to easily one shot anyone, plus cooldown reduction to clear waves with Q.
Both builds are fine in my mind, but I as a player like to try to win lane with Cho, and get a early kill or two, and try to snowball ahead.
Sorry for the essay, lol, I tend to have a lot to say about cho, since I play him so much. However, take into account that I am only Gold, and that my opinion on builds are far from absolute truth.