I think W should be leveled last now, it only adds .4 seconds to the snare at max level. Q is going to be your main damage and harass. E has more wave clear and is going to reduce more MR as it is leveled. But W seems underwhelming now as you level it up. It's definitely more of a flex level up as is. E is going to make more of an impact later in the game as it is a percent MR shred so that would imply leveling it later. But W vs E is a tough call.
As far as the Q skillshot problem. I would say leveling E second might help in that matter. Optimally, you will want to unleash hell when your passive is ready and when your ult is up. If your opponent is near minions E first (procing the passive), activate your R in transit. The Ult will cause a splash effect from the E initial hit and then the E will hit the surrounding minions before coming back to the original target and then it will splash again clearing (possibly) the minions around the champion you are targeting, if it doesn't, use your W and that might do it. Proceed to double tap Q on your enemy, E again, then QQ again. In teamfights, you will help take down tanks with your E and Qs, but if you want to hit the carries, you will have to use better positioning than old Ryze.