If you were Kitty Ping of pern fame, and had metasynth to play with genetics and a bunch of firelizards to mess around with...
What would YOU have done with their genes, instead of what she's done? There were mistakes along the way, creating the near-blind whers, and then the out of control crazy sizeness of them later, and this fascination with the 5 colors.
If you had the controls, what'd be your goal for long-term engineering of the base stock fire lizards? Knowing that Thread would fall, and they could fight it somehow - but they don't have to be the only method.
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Obviously, I wouldn't go for size. Smaller is better, the size thing is retarded imho.

I'd also change the requirement to human-bond. Perhaps an affinity, but a slavelike tie to their human? When dragons could just as easily bond each other, or have multiple connections and be 'flown' from one person down on the ground telling the others what to do? (which is what the Zekiran dragons do.)
Less concentration on color rankings, and more on ability-ranks. Who cares who's gold - if she can fly and produce fire? or the 3 greens who race into the air and scout, providing a heads up to many small villages without the huge uproar that a gigantic queen causes.
Probably lastly, change the 'fire' to a more 'napalm' like substance, which ignites upon contact with the Thread substance. it's biological in nature (sort of) so it could be 'coded' into the release of this gas or particle spray, and on contact fizzle into bursts which then take out surrounding bits of Thread.
So instead of having 20 gigantic dragons and 80 or so people to work with them (just a guess at 4 per dragon like my one slightly delayed clutch takes) you'd have 80 tiny dragons and their riders, and *that's it* for the Thread that 'fall.
.... Just tryin to get the juices flowing. Had a little fantasy the other day about going to Pern, yadda yadda. I'm like that. So what would you do if you had the gene-altering metasynth?