Good question Freestone. I've seen that question come up before. The first issue is that our native cutthroats did not evolve in competition with any other trout species. So they don't compete with them. We could stock massive numbers of cutthroats in the Colorado River mainstem and we would rarely see them again. For the most part they would just disappear. The only place they we can stock them and they will be successful is in waters that are occupied by only cutthroats.
Theoretically, you could give them a better chance by raising them to larger sizes before stocking them. Here's the problem with that: cutthroats are a wild species, not domesticated. Rainbows have been heavily selectively bred to have domesticated characteristics. So to produce 1,000 cutthroats that are 12" would be vastly more time-consuming and expensive than producing the same number and size of rainbows. Because they're wild, cutthroats spawn at a specific time of year, in a fairly narrow window (say three weeks). Rainbows have been manipulated to produce eggs over a wide range of timing in order to fill gaps in hatchery production. So you would have a huge amount of hatchery space sitting empty for big portions of the year if you switched over to focusing on growing large cutthroats for stocking. You'd have hatchery personnel sitting around twiddling their thumbs looking at empty raceways.
It's also a question of scale. Just as an example, I ran a couple of quick queries in our database for the year 2010. In that year, statewide we stocked a total of 619,985 Colorado River cutthroats, with an overall average length of 1.9", or 5,252 pounds of fish. That same year we stocked 9,139,081 rainbow trout averaging 6", or 1,625,297 pounds. We actually stock very few rainbows that are 6" -- but we stock a lot that are 10" and a lot that are 3" so you get the average in between.
So on a weight basis, we stocked about 309 times the poundage of rainbows than we did cutthroats. If we were to make some kind of huge shift in the allocation of our hatchery production to cutthroats, we simply wouldn't have the eggs to produce the kind of numbers of fish required.
You could theoretically take some steps back and start modifying cutthroats in all the same ways that rainbows have been modified -- you could get them to spawn over a wider range of dates, grow faster, be more aggressive and competitive toward other species, be more tolerant of crowding and resistant to certain diseases, etc. But at the end you would have a fish that does not reflect the native fish of Colorado any more.
It really comes down to basic goals. The basic goal of our cutthroat program is to perpetuate genetically pure populations of the fish that are native to Colorado, and have them reproducing and sustaining themselves in places on the landscape where they're able to. The goal of our rainbow program is to provide the most recreational opportunity possible, pure and simple. There is not a lot of overlap in those two strategies.