I prefer N-air and jab, since they are safer.
That's actually not true at all, and that thinking is why I believe most Ike's lose to MK. It requires a matchup specific strategy, as you can't simply space with aerials like every other matchup because of MK's top class ground speed and grab game.
If nair hits his shield (even perfectly spaced), he can tilt you out of it, grab you, or he can loop you (EASILY); many ways putting Ike into the place he doesn't want to be (above MK). If Nair doesn't hit his shield, it's fairly easy for him to time a dash attack or shieldgrab before you can jab or outspace you with fair.
Even if you hit with nair, unless it's at low percents you have no real follow ups as MK can simply fly away, or get to the ledge, or nado, or easily air dodge past you to switch the position. High risk for little reward.
I believe the key to the matchup is staying on the ground as much as possible.
That being said, said play revolves around proper pivot grabbing. Done far enough away, it's an entirely safe option and stuffs the quick grabs and dash attacks that are half of MKs ground game and advantages on Ike.
http://www.youtube.com/watch?v=RPeHWWV2X8w
Since nobody has any tips, I'll review the concept myself by bouncing ideas off you guys for maximum brainstorming. For the purposes of using the video (critiquing myself I guess rofl), I'll point out its uses in it. I'm aware that I overused it for the sake of testing its application, but the amount of times it paid off or went unpunished says something for itself.
Examples of punished (aka poorly spaced) PGs:
0:41 (MK was way too close, that distance is to MK's advantage so I should have ran further)
2:24 (too close again, but doing it twice in a row was a called mixup.) Only twice in the whole video, neat.
Excellent PGs:
0:06: Let
know it was jam time.
0:50. Most players know about nair to bair, but PG adds an extra option to add to the end of the chain which covers the bair that people often try to punish (Ike landing facing away).
1:29 PG counters air dodging to the ground perfectly btw.
1:43 I called the approach, but was too far. Still, my cooldown was faster and I got a free jab, always nice.
The bottom guideline I've found however, is that if you initiate the PG outside of MK's ftilt range, it's unpunishable and the only thing you lose is ground. Meanwhile, if you called the MK's running grab or dash attack, he gets 10%+ (<3 Ike pummel). If you have ground to spare, use it.
It's incredibly quick, and the range and hitbox window are deceptive. When used properly, there's no way for MK to punish it in time as you'll already be facing the direction to jab right away. What makes it so amazing is that it's basically an unpunishable version of sidedodge for dealing with grabs, which is an amazing gift.
It actually plays right into the Ike's hands when MK tries to bait to punish it by dashing in, as a pivot grab easily turns into another pivot grab which stuffs the approach. Happens all the time, and it's hilarious.
The threat of being pivot grabbed will consistently make MK's hesitate to approach on the ground or even follow up. Running up to Ike and shielding is no longer an instant win, and many will be tempted to try a more aerial approach to which Ike has far more tools to deal with (bair, fair, utilt, aether). All great things to happen for Ike, and makes the matchup playable.
And oh man, Ike's have got to stop running around so much.
WALK, it's the perfect mixup to just spamming run and shield.
Edit: On a side note, PG also works great on Snake when you're right outside his ftilt range, as he'll often try to mortar dash away.