When I think of them working together on the mountain, I think it would have worked. They were symbiotic. They balanced each other. Think of the scene where their sheep get mixed up with the Chilean ones... Jack cursing Aguirre, Ennis being reasonable and telling him they just had to see it through. And then Jack accepts that because Ennis has a steadying influence on him.
I especially love how there are many instances, on the mountain, where Ennis looks after Jack... ordering soup, killing the elk, switching places, trying to set the tent up right. Of course it's reciprocated.. there are so many ways in which Jack looks after Ennis, too - getting him to open up, guiding and reassuring him through the second tent scene. Beautifully symbiotic, and really much more equal than their relationship becomes later on.
Later, I see more bickering, withholding, denial. I think there is certainly, ABSOLUTELY the potential that it 'would have worked'. I would hope that if they were living together and working together, they would fall into that easy partnership that they had up on the mountain. But I suppose a lot would depend on external circumstances and pressures, too.
Personally, though, I don't think the ultimate measure of whether something 'works out' is the living happily ever after. I think people come together because there is a reason behind their connection. They have something to learn from one another. Sometimes that ends before one's life ends, but that doesn't necessarily mean things didn't
'work out'. It might just mean the impetus behind your connection with that person has been fulfilled and has therefore ended. I think Jack and Ennis were learning from each other right up until Jack's death, and for Ennis, even afterwards. It didn't work out the way Jack wanted it to and no one can say for sure if it would have, but clearly something 'worked'...