I have to agree with the Templar Rage. Ike's obvious weaknesses are his speed, recovery, and lag. Most of his moves have to be timed well to be used well, due to the slow swings and the pre and post lag.
Although that all has to do with being able to predict your opponent's next course of action. If you can do that you forget all about speed.
Next is his recovery, which is his biggest flaw IMO. His >+B seems really good because it can go extremely far horizontally, but I have ran into a terrible flaw in this ability (which many others have realized too). If someone jumps off and runs into you purposefully before you are close to the edge you will attack them and then be unable to do anything as you fall to your death. This also applies to ledgehogging.
His ^+B is good for vertical recovery, and fighting off edgeguarders, but it is still easy to see it coming and counter it.
As this current time the hardest person for me to fight is Samus, due to her ability to keep away from people. Fox isn't as much to worry about as people say, because his laser doesn't really do much, just a little % add, at least compared to Falco's, which can flinch you at any time.
BTW, never play Skyworld with Ike, you will kill yourself... constantly. Aether seems to destroy most of the platforms before you can grab them.