UAL Corp (Nasdaq: UAUA) has agreed to merge with Continental Airlines (NYSE: CAL). Much as we wish it weren't so, this means bad news is brewing for Boeing (NYSE: BA).

Why? UAL Corp, aka United Airlines, has dominated the headlines in recent months. Before its tie-up with Continental, there was the ill-fated merger attempt with US Airways (NYSE: LCC). But before that, United played the villain to Boeing shareholders when it held up the company at metaphorical gunpoint, demanding that the plane maker enter into a bidding war with archrival Airbus for the right to sell United up to 150 new wide-body airplanes.

Ultimately, neither side agreed to play ball, and United ended up splitting its order between the two manufacturing giants. But it's going to be a whole lot tougher for Boeing to play coy next time around. UAL was the company doing the hunting, will end up with 55% of the new company, and as indicated by the fact that post-merger, will retain the United name.

All mergers are equal, but some are more equal than others
However, things might not be so bad for Boeing seeing as how Continental's CEO, Jeff Smisek, is the one keeping his job as head of the new airline. Continental is currently all Boeing, all the time. UAL operates a diverse fleet and in terms of backlog it's actually the other way around. While it split the wide-body order last year, United has nearly three times the number of Airbus planes on order than it has undelivered Boeing's waiting in the wings -- and the Airbus orders are worth more than twice the dollar value flowing to Boeing.

Now here's where things get potentially really bad for Boeing: As usual in deals like this one, the key participants are promising to present their shareholders with "synergies" from the merger. Translated into English, that means "cost cutting and fewer flights." And more pertinent to Boeing shareholders, it could mean both fewer planes purchased, and more hardball negotiating on the purchase price. Will the combined enterprise need 50 new 787 Dreamliners? With Boeing now having one fewer customer in its order book, United's negotiating position is going to get a whole lot stronger post-merger.

Foolish takeaway
Investors are bidding up Boeing shares post-merger news. But it looks to me like they're boarding the wrong plane.

Fool contributor Rich Smith does not own shares of any company named above. The Motley Fool has a disclosure policy.