That's the thing you have to remember though, there are two classifications of junglers in LoL.
Junglers like Lee Sin and Nocturne are fantastic because they allow for an early game snowball in the other lanes, thus giving the advantage to your team before the end of the laning phase. That's why Ezreal is FOTM right now, actually, it's because he has such a powerful laning phase that he's able to shut down other carries and prevent them from reaching their late game potential. These characters typically don't have as great a presence late game unless they get fed, and they rely on dealing their damage early game.
Junglers like Skarner, Shyvana, Amumu, and Cho'gath are farmers, junglers that don't have ganks as good as others, but contribute WAAAAAAAAAY more to their team once the laning phase is over. Amumu and Shyvana have ultimates that change teamfights and are very capable of winning games in the right hands, with proper team coordination. These characters rely on enduring the early game so that once the laning phase is over, they'll be a terror to the enemy team. Shyvana has the added bonus of being able to hunt down enemy junglers, because she's such an insanely powerful 1v1 duelest. Thus, I take her against hard gankers like Nocturne, and I go jungler hunting. This prevents the early game snowball that hard gankers are banking on, AND it basically wins my lanes for me, because if your lanes brought some form of hard CC with them (Ahri's charm or Taric's dazzle), Shyvana ganks can wreck because of how much damage she puts out.
Shyvana has her place in the proper team compositions, just like EVERY jungler. I especially love jungling Shyvana with an Irellia up top, because Irellia specializes in conning enemies into thinking that they've won a fight, before suddenly flipping things around and wrecking them.