I've done a lot of both of those routes (but not the Kettle Valley).
You can't go wrong, they are both fantastic, and the time of year you have selected is great. By mid/late September there is a chance of some winter-like weather in the high mountains in Colorado, but if you can wait a day or two for storms to blow through you can still catch great weather most of the time.
If you choose the Rockies, please try to make time for Banff to Jasper, one of the most beautiful stretches of road I've ever been on. And also try to ride Logan Pass (= Going to the Sun Road) through Glacier National Park.
Once you get to Walden, the TransAmerica route sends you due south to hit the Hwy 70 corridor.
Instead, I would recommend going through Rocky Mountain National Park - you can bear east from Granby and ride Trail Ridge Road through Rocky Mountain National Park (highest paved pass in USA at 12,200 feet)
OR if you don't wand to go that high, stay a bit north heading east on Hwy 14 out of Walden through the Poudre Canyon (10,000 foot pass) and then head south along the front range (Ft. Collin - Loveland - Boulder - Denver).
See Adv. Cycl. Great Parks North Map 6 for a suggested route from Granby to Denver via the park. Once you get on the Peak to Peak highway (the east side of that loop) there are several alternative ways to drop down out of the mountains if the weather is bad, or you can get out of the park to Ft. Collins.
If you choose the Pacific Coast, please try to ride the section south of San Francisco to at least Santa Barbara. The section between Monterrey and San Simeon is spectacular.
Peak to peak highway last week:
Near Jasper Canada summer 2008:
Big Sur a few years ago: