Ike's Jab is actually all he has in this MU. Well, and Quick Draw and Bair.
If you think QD is a bad move, you know nothing about Ike. Leave this thread now. Quick Draw is amazing against Marth, ESPECIALLY ON FD. If Ike charges QD from a range, Marth has NO options except jump or grab the ledge to evade damage, unless he is out of range, and it still forces Marth into the air. From there, Ike releases QD and is now inside Marth, with little to no lag. QD also ***** airdodges (M2k showed me how to do this really frikken good).
If your opponent charges QD, jump onto a platform and move towards them, attacking them from above with a Fair, this will force them to QD away (which resets the situation, dun, dun), but eventually your speed will allow you to close in on Ike. Your shield is limited, so if Ike just holds QD, your shield is no good unless you're really close already in which case the Ike shouldn't be using QD.
When Ike is in the air, don't swing right away. Wait for him to do an action, then react to it. It doesn't matter if your reaction time is slow. Ike is really slow. He also can't do two aerials in one SH, so if he jumps, wait for an action.
Don't try and punish Nair on shield. Dancing Blade outspaces Jab, so you can punish Fair with Dancing Blade, and punish everything else with Dancing Blade (unless, you're fighting Renegade's Ike, in which case he will always SDI out of hit two).
You can grab the edge, and counter aether on reaction over and over. It's the easiest way to gimp Ike.
Basically, the move to watch out for is jab. Get into your own spacing, and apply pressure with Fair, Dtilt, and Dancing Blade, like any regular MU. If you get in close range, shield and roll out. Don't challenge the jab, and you'll save a lot of percent not fighting Ike's only good option.
Don't throw kill moves, and Ike will be hard pressed to ever land a hit, so long as you're playing safe and patient.