Yeah, Link is actually one of the most annoying characters to get a good counter for. His ground Up-B is more broken than 40 well-timed Forward Smashes by Bowser. Ganondorf is actually a good choice, as he can counter most of his moves. Cancel out his Boomerang with your Forward A, and you have the dodging speed to roll around Link. Ganondorf also isn't that slow in running speed(surprisingly so...but then again, Bowser has good running speed too...erm...mediocre.)
Practice Shield Reflecting, and Power Blocking, then your enemy won't stand a chance. Frankly, Link can't stand up to the advanced moves, even when he uses 'em. If you can't...good luck!
As for the Doc...heh. Link may actually work well in this case. His Up B can't really be turned around. But of course...almost all of his other moves can. He can't edge guard easily, and Pills aren't that hard to dodge or reflect(sweetly enough) If that doesn't work, try Falcon or Ganondorf. Basically, any move that clears out both sides(which MANY characters have) can do serious damage to Dr. Mario. Peach may even be a decent choice...unless he uses that can on your recovery. Hard to grab the edge when you're TURNED AROUND!!