Didn't counter pick? The lux was lower in pick order. Go to punish the failed q? Flash -> E + W or E + W + R or either one without flash she was probably initiating the trade at max distance for the q anyway. Dodged the E at point blank? grats, still have to break through the w shield to get a even trade. You can burst her to death through all that? She's locked the lane at her turret and is playing passive + built a zhonya's or she's at max range for q in the back line and positioned between peel and cc. Your an adc? She initiated in the fog of war and bot lane communicated where you warded.
There are multiple problems with lux that make her a headache to lane against . The first being just one mistake on a mid - late game lux that has went even is most likely going to make you back or kill you unless you got really fed off roams. The second problem is she has a lot of room to get out of punishment for mistakes with her slow, snare, and shield. The third problem is her counter matchups are literally a 50% win rate there is nearly no pick to skew the lane in your advantage (Excluding galio) . Oh and the final problem I'll mention is lux has a relatively easy kit to pickup and get used too a champion with so many plus sides really needs a better skill floor than hit the large projectiles q/e and then r.
A simple answer to make her less annoying is shorten the range and area of her E, give q a slightly shorter range, give the R a longer cooldown + make it interruptible, and just completely remove W by reworking it into another attack or control skill . Make her a risky immobile burst / zone mage . Oh, I almost forgot one other change make her base damage low and buff up the ratios some so she's more item dependent to do damage. Instead of 500 + 75% ap on the ult make it 400 + 100% ap give or take some and do the same with q (Low end of a possible change, on the extreme end they could make it 150 + 300% ap which would gut lux support's early game ) (This really wouldn't change much, both her main roles generally build pure damage).
She's not really op. However, she is currently a headache to play against.
Note: :P such a long post I'm pretty sure if I didn't use a simple list form / rambling approach , I could of composed an actual essay detailing why lux is hated and possible avenues that could be taken to resolve it.