I imagine Ike will wander in on his own accord. If they added the Greil Mercenaries in, they would need 9 models (plus Mia, if you want to count RD), which would take a lot of time for a 5-second cameo in SE.
I can see Ike being teamed up with Samus. It seems that the pairings so far are pretty complementary to one another, and Ike's close-range power coupled with Samus' long range (and speed as Zamus) would make a good team.
The perfect introduction for Ike: He's standing on the edge of a cliff, in that badass pose with his sword stuck into the ground and cape blowing in the wind. He sees the detonation of a Subspace bomb in the valley below, grabs his sword, and runs off toward it.
Near the edge of the explosion, he finds a few wounded generic enemies (Goombas and Octoroks and the like), as well as Samus, who was fighting a giant Dodongo. The Subspace bomb destroyed Samus' suit, leaving her as Zamus, as well as her ship, though she was able to send a distress signal on multiple frequencies (which would prompt Fox and Captain Falcon into action later in the story). Ike agrees to travel with Zamus, and together, they'll find the maker of the strange bombs and restore the area to normal.