Yeah, here's my list of thoughts on Ike's weaknesses.
Slower Attacks: Bar his Nair in some cases, his moves are slow and don't punch throw things without good precision, so characters can easily stuff and overwhelm him, leading to him being rather juggle-able.
Bad OoS options: Obvious, said to death and entirely true.
Average CC options: His best CC options are CC into Grab and CC into D-Smash, both are good options, but they aren't the instant reversals of other characters or have great range to deal with a poke (like DK or Boozer)
Linear Recovery and Laggy Recovery: Ike can only recover either entirely Vertically or Horizontally, so it's really obvious which of his two recovery options he'll pick. He has some mix-ups at times with the wall-jump or how Aether can be used to stuff an onstage edgeguard, which is nice- buuuuut. For QD, he's very easily stuffed mid-air since he can't have a hitbox out unless he's close to the ledge, otherwise hitting you with QD attack leads to his death. For Aether, there are two massive problems in it, where Aether has a blind spot at the peak which characters like Marth(or anyone with a large attack that won't get hit by Aether's upswing) can easily swat off, sometimes even if Ike tries to sweetspot. On the other hand, it's easy to steal his ledge and force him to get on stage, and he suffers from a lot of lag on stage. So much so that, as an example, Peach can do a +100% normal get-up and still D-Smash him off stage and into death.
Lack of Stage Presence: Because Ike has slow and precise moves, Ike spends more time moving and not attacking than other characters do, meaning he has a lot of trouble holding center stage, especially against projectile characters. This problem, in a way, is an amalgamation of the other problems.