what? no what you've gotta do is drop the flare before you pop beast within and then put like SERPENT STING on them or some shit and get your pet on them. at that point the rogue will have to sprint away and vanish but he'll have to pop clos to get rid of serpent sting aaaand with your pet on him and the general unreliability of vanish, and the haziness of how it works with pets, there's actually an overwhelming chance it will bring him out of stealth, and there's not really anything you as a rogue can do about it since the pet can't be cc'd, so you can't even gouge and vanish.
also it's not especially difficult to catch one in stealth with a flare. even with sprint you can't move especially quickly and you stand a pretty good chance of getting him just from firing it in some random area that was relatively close to where he vanished.
pet unstealthing is fairly unreliable, plus if the pet does unstealth him can't he just do prep/re-vanish? (not sure if that stops the pet following). flare is a great tool but it is on a 20 second cooldown so if you don't catch them in that one flare (and good rogues i've met don't move while vanished in a PREDICTABLE fashion, so you gotta be lightning quick on your flare button) they're free to open up a stunlock on you again. hunters are particularly fucked in arena since flare doesn't GO ROUND pillars.
basically when TBW is active yeah it's a godsend against the rogue since you can actually get some damage in and not get stunned/slowed all the time, but the fact that rogues have so many cooldowns and when they run out they can just PREPARATION and do it all again means it won't really get you anywhere. they have too much survivability so it's not always possible to bring them down to a level where, once TBW is over, you have a good chance of killing them.
aside from shadowstep, there's deadly throw, evasion which means wing clip will fail 9 times out of 10, clos for frost trap, my concussive shot is a 4 second slowing ability compared to a rogue's slows, which are 70% and continuously reapplied if they're hitting you at all, and let's not forget cheat death, which is bugged as fuck, so if they are CLOSE TO DEATH they can still fucking mash you up pretty badly or some kind healer can burn a big heal on them and THAT is fucking frustrating.
idk i never played 20/0/41 because shadowstep still blew when i was playing my rogue but it sounds like you aren't playing it the right way at all if you think it ends at NAH HE JUST RUNS AWAY AND WAITS
well, now, shadowstep is just overpowered imo. i've watched mark duel a lot of rogues on his frost mage (he is a good mage) and it's just unbelievable that mage, a class with such escape mechanisms that used to beat rogues reasonably well before now just gets ANTI-KITED by a rogue. basically classes that rely on kiting, apart from possibly non-feral druids (ferals can actually do pretty good against them), don't really have much of a chance against a rogue anymore.
i don't know maybe i'm just a BAD HUNTER.