Lux's E is monstrously mana-hungry. At rank 3, it costs as much as her ult. At 5, it takes 130 mana per cast. If Lux rushes E, she's going to have a lot of early game mana issues.
Anyone who can readily dodge her E is going to be a problem; Fizz, Katarina, Zed, Talon, LeBlanc. Anyone with comparable range to her is going to similarly have an easier time dodging her E; Xerath, Ziggs, Viktor.
Is Lux strong? Sure, I don't think anyone would really contest the fact that, when things go her way, Lux can drop a lot of damage in a short period of time. Thunderlords did not do anything to mitigate this fact.
Do I think Lux is balanced? Yes. She has a number of counter play options available to take her out. The single biggest problem is that people do not capitalize on her early game mana problems. At lv 2, her Q-E combo costs 120 mana; that's almost a third of her mana without items. Champions with no ability costs (Katarina) or rapidly regening energy (Zed) that can use their own abilities freely and who can continuously dodge such combos from Lux are going to force her to rapidly expend her mana. That puts her back against the wall. Like most mids, Lux is very vulnerable to burst damage and CC.
In a pure skill match-up, if an assassin with a blink goes up against Lux, she'll lose almost every single time. Because she either tries to use her Q at range, at which point they blink or step to the side, or she tries to use it when they're almost on top of her, at which point she still runs into the risk of the aforementioned blink dodge.
Also, it's worth noting that while Lux has a high win percentage right now, she's middle of the pack for average kills per game.