Intamin was still the industry leader at the time when it came to innovation, and they were probably cheapest.
Sorry to re-bump this already-bumped thread, but it may very well be that MagnesiumPC hit the nail on the head here. It is a trick sometimes used in the construction industry, pricing oneself to the point of economic losses to win an important contract. Not for the money and not for the love of the sport, but to build a portfolio. It just dawned on me that I have heard of an example of this before. A few days ago, actually, talking to a friend in the construction industry.
So, there's this great engineering/consulting company in Oslo. Not among the biggest in the industry, but they have expanded a lot in recent years and apparently want to size up to be able to compete for the most high-profile contracts. They have a lot of experienced people, who they hire out on a project-by-project basis to other consulting companies, but very few in-house projects. It's a decent model, spreading one's work force to build reputation and experience, but without the company having to compete for projects. They bring experts to the projects and take care of the HR side of things, the other company gets to rent people temporarily without having to find work for them after the project is over.
But now, the company's strategy is changing. They employ people with very good project records and impressive CVs, but very little of this goes back to the company itself. "We provided a few guys who did crucial work on the Munch museum for another company" sounds a lot less impressive than "We did crucial work on the Munch museum." So they decide to gather their people for an in-house project, rather than spreading them across other projects to work for other companies. This time, they want their own name on the great banner outside the construction site. With references like that, they would be more sought-after for future projects, and a more prestigious employer for great minds in the industry.
Then a great new project comes up. The Viking Ship museum, one of the crown jewels of Oslo's tourist destinations, is up for a major overhaul (about time, the last big one was in 1934 to my knowledge). All over the industry, people know that Multiconsult did the Munch Museum, Norconsult did the Holmenkollen Ski Jump (both companies feature the landmarks extensively on their promotional material and in recruitment videos), now our ambitious consulting company wants a project like that on their recruitment posters as well. But thing is, all the other consulting companies have also put in bids for the project.
What does our little company do then? Declare that they want the museum contract no matter what. They put their bid ridiculously low, meaning they won't earn a penny on the contract in the short run. Probably losing a million pounds or so, when all is said and done. All the other companies are in it for the prestige, yes, but they also want to make money off of it. So nobody can match our heroes when it comes to price, and the builder (Oslo Municipality, law-bound to go for the lowest serious bid) ends up picking them.
Back to Millennium Force, I suspect that Intamin did it this way. Cedar Point put out an invitation for bids to build their next big coaster, and all the regulars put in their bids. Morgan wanted this-and-that, Arrow wanted so-and-such, B&M might have abstained, and Intamin decided that 80 % or so of a reasonable price was high enough. With what was at the time intended to be the world's tallest and fastest coaster, Intamin secured a name for themselves in the industry (beyond what they had already), good relations with Cedar Fair, and established a foothold in the Mega Coaster segment. "We built Millennium Force, we're the right people for your project" is a great byline. Apparently it worked, since Intamin Hypers really got a boost after Millennium Force, and Cedar Point came back to Intamin when it was time to take the height record home again.
This is unfounded speculation, though, and it could very well be that there was a different reason entirely. After all, Morgan did go for an even bigger project in Steel Dragon 2000, and Arrow had X coming up around that time. It could simply be that the other candidates were busy. But an un-and-coming company taking a loss project to build prestige certainly isn't unheard of either. I bet there are plenty of examples from other industries as well.