Situation: I had 1 player cancel at the last minute last night just as the party was about to fight Ike and co. So I had 2 players and no cohorts. Was going to be a slaughter. One of my players suggested we gestalt the classes as an experiment. Did just that as technically that would mean I had the power of 4 characters on the board.
What happened: The two characters held their own but ultimetly it was a losing battle. Even though they were gestalted they still really only got 2 rounds out of 10 since the enemy had 8 players on the board (Ike, wraith, baatuzi and 5 zombies). It was a valiant effort but doomed to failure. And my two player were overwhelmed by the choices gestalting gave them. I ended the session early as no one was having fun and determined the whole thing was a dream or alternate realty version of events.
Aftermath: Now I am going to reply this battle when the full compliment of members next meets up. But two of my players know what’s waiting for them and some of the tactics used etc. Any suggestions on changing that final battle with Ike in such a way to make it different without losing the flavour?
One important thing to remember about gestalt characters is that they're more equivalent to 1.2x to 1.3x (depending on level and the classes mixed), not 2x the power of a single PC. While they can have good saves all around, higher hit points and full abilities from two different classes, they don't necessarily get double the hit points or feats, and they certainly don't get twice as many attacks or deal twice as much damage.
Maybe switch from the "Death" theme of the temple to the "Magic" theme. Swap the zombies for some golems. Maybe change the demon/devil to be a different type.
Let Ike have a simulacrum. The players break into the temple where Ike greets them on the first level. He explains that everything is fine, surrenders, etc. trying to convince the party that everything is OK and leave.
Maybe switch from the "Death" theme of the temple to the "Magic" theme. Swap the zombies for some golems. Maybe change the demon/devil to be a different type.
Let Ike have a simulacrum. The players break into the temple where Ike greets them on the first level. He explains that everything is fine, surrenders, etc. trying to convince the party that everything is OK and leave.
That’s actually a good idea. Maybe turn ike into a mage/priest. Wasn’t there a prc which let you do exactly that? And the zombies into a spellstiched zombie. May even resurrect Aushana and have her flirting about or look in the baatuzi codex for something appropriate.
The party absolutely hated the dread wraith and it was the most dangerous opponent as its first hit it drained 8 con, was difficult to hit and kept springing attack from the walls. The zombies they could nullify to a certain degree by moving, the devil really didn’t do a lot of damage though it did hit a lot. That left ike as the next most dangerous opponent and since his flamestrike was nullified by a protection from energy spell and they all their saves vs his death affects he was somewhat less effective than the wraith in the end.
So definitely keeping the wraith 
You are also right about the gestalt. It was the first time I used them and they seemed to be “double strength” characters on paper. But in practice x1.3~1.5 is a better estimation.
What I ended up doing is leaving the monsters the same but using a different map with more tactical problems to deal with. I ended up using the “Fane of Lolth” minimap and turned the zombies into statues which turn into zombies. Since I also only had 3 pcs and 1 cohort on the board at the time the new map allowed me to stagger the attacks of the monsters without looking too contrived.