The top 3 all have something ridiculous about them, but they are not unbeatable, and their dominance mostly comes out against the low-tiers. Nu I think just has too many tools. Arakune can lock you down too easily, and his overhead loop and do 7k damage without meter. To mention a couple things. As for Rachel …
I main Rachel, and can talk on her some.
She’s more difficult than anyone else I picked up in this game (which is nearly everyone except Carl), or in any fighter I’ve played in a long time. Could have just been me, but I really had trouble getting the hang of her for the first couple months. She’s very punishable if you make mistakes, she’s slow until you really get used to her, and she can be pressured relentlessly. She’s trash when it comes to a defensive game, and has no great reversals (though 6a is ridiculous on certain characters … like Arakune). Her fireball zoning can be annoying, but most characters have definite ways of making you pay for abusing fireballs.
So she’s kind of an all or nothing character. Nuts on offense, crap on defense. Most matches I have against good players result in me barely getting in at all, or killing them pretty fast. Personally, I think her biggest issue is her damage, and her guard break. I think she’d be fine if both were scaled back. The nerf she appears to be getting in CS is hard enough that I really don’t see the point in picking up a character that’s so difficult to get really solid with. But who knows if all of that will stick.
To people having trouble against her, rush her down. Stay in her face, do everything you can to keep her from starting her pressure game, and do not early burst. I don’t play online much, but when I do, I’m amazed at how much people early burst against her. Once you do that, if she has meter, one counter-fork and you are fucked.
Anyway, I can see why she’s top tier, because in the right hands she is relentless and insanely strong. But it isn’t always easy to do, and I don’t see lots of people who can really do it well. Her top slot mostly becomes apparent in high level tournaments.