Had the merger gone through there would have been no Spirit to fail.
There would have been a JetBlue/Spirit to fail.
An integrated company might have meant Jet Blue would be in a better position than it is.
Or it might have been worse.
At the point where JetBlue and Spirit merged, JetBlue would have taken on Spirit's massive debt - $8 billion dollars. JetBlue makes a total of $9 billion a year total - which means they'd have to divert every single penny of their revenue for an entire year (without paying for fuel, pilots, maintenance) to pay it off.
How long would it take if they just took it out of Jetblue's profits? Forever. JetBlue is currently losing $1.2 billion a year.
How long would it take if they could repeat their best years ever for the next decade? The best year JetBlue had occurred about ten years ago, where they made about $1 billion. It would take them eight years, during which they would not be able to reinvest in the company or do any of the other things (other than operation) that you need money for.
So why would they even propose it, if they would take such a massive hit? Two main reasons -
One, you get some small economies of scale. But they are small. You might be able to reduce standby crews or overnight counter workers - but since both companies run their employees as hard as they can to begin with, you can't get rid of (say) half the pilots or half the gate agents from Spirit to make it cheaper.
Two - and this is the big one - you get their routes. Airlines generally charge the lowest price they can per route to be competitive. Thus the most profitable routes are routes that have no other competition. There's so much air travel now that there aren't many of them, and they are generally local (flights into Islip Long Island, to use an example.) But they are also short, and those also have competition from driving/buses/trains.
If the merger results in JetBlue owning both popular routes between two airports, they can significantly increase prices (and thus revenue) on that route - because now they have no competition. They WILL have competition once other carriers take over that route, but for the time that other carriers take to adjust (months, perhaps a few years) they have something of a monopoly. Thus, there is a window during which they could potentially make a lot of money.
Now, it should be noted that this is not good for consumers, because it results in a significant increase in ticket costs. And since JetBlue will start moving away from Spirit's model (which is the cheapest tickets period) the rest of their tickets will rise in price as well. Which means fewer people can fly, those that do will pay more, and inflation will (slightly) increase. But for that short time they could make more money, which may make such a merger worth it. And if they then drop prices slightly, they might even be able to keep those routes - JetBlue is a "hybrid" airline that charges more than discount airlines for a perceived increase in quality (legroom, better first class etc.) So people may pay more even on those former Spirit routes.
But that's all a big assumption. Would it have worked out? With the rapid rise of jet fuel, it would certainly have been a HUGE blow to the new hybrid airline. JetBlue (and every airline out there actually) is already struggling; taking on all that debt with the (now-slight) rise in income would have likely been a deathblow.
Compare that to the recent Alaska/Hawaiian merger. Hawaiian came in with $900M in debt - about 10% of what Spirit had. And neither Hawaiian nor Alaska is a discount airline, so they don't have as much price pressure. And even so, they posted $193 million in losses in Q1 2016. Will they survive? They have a much better chance, because they have 10% of the debt to pay off, and can probably deal with a few years of losses before having to shut down. And after a few years, it is likely that 1) fuel prices will come down or 2) fuel prices will drive price of ALL airfares up, and they can then charge more.
I suspect there are a lot of JetBlue employees are breathing a sigh of relief today.