Can't kill the illusions before they reach your base because they move too fast due to manta/travel/drums(removed later on) speed. While you can dominate early and mid, naga is very good at finding farm regardless so you also need a lineup that can actually end the game quickly.
I mean, just look at how many teams lose to a naga even though they were winning. Good teams too. Happens all the fucking time. Kill naga, prevent her from jungling, she gets a 25+mins naked radiance. And she still turns it around at 35mins quite often.
I didn't have as much of a problem with PL when PL was all the shit because PL only does one thing. He makes illusions and overwhelms you. That's his thing and literally all his skills are built around this simple concept. Also PL has a huge ramp time, he's pretty fucking awful for a long time, because well he's a pure illusion hero and illusions suck early on. Naga is a lot more retarded in my opinion because her illusions are made on demand(no RNG, no need to actually attack shit on the way) but also because her other skills are extremely good. Ensnare is one of the very few CC that goes through BKB and interupt TP, Song is one of the strongest ultimate in the game in terms of teamfight control/initiation/disengaging/counter initiation and Riptide is a meh spell if not for the fact you get your illusions to cast it, making the illusions deadlier and push harder. When you gank her it's not like PL where all you have to bring is a gem or a sentry to see him, you need to absolutely make sure to disable her the entire time or she songs and get the fuck out. It means you need several heroes with disables to do it, which puts in a shit spot if she's been pushing all your lanes and quite often killing her gives you exactly 0 advantage since you have to go back, push all your lanes back and by the time you're done she has 20secs left to rez. Only thing you get is roshan, sometimes, but if she buys back you need to bkb to even loot roshan in case she uses song.
I'm all for the hero being strong as fuck. Many heroes are, that's fine. I don't like the proxy pushing and herpderp illusions a click. The fact you have to dedicate your carry to actually dealing with her illusions a clicking your base and that's somehow an acceptable counter is retarded. Illusions should be for farming and for teamfights/confusion, not for base pushing while you're sitting halfway across the map. If wolves or treants scaled with items, I don't think they'd be as easy to use as they are now, but that's pretty much naga illusions(riptide balances out the fact illusions are fairly shit compared to treants/wolves early on).