This may be to late for your trip but I've ridden both many times since I live in Skagit Valley and the S. Skagit Hwy. is a much better ride. The old highway takes you further away from city sounds (hwy20) and puts you in farmland, riverside views and the hillsides. The Cascade Trail has a lot of stops for roads and driveways not to mention some dogs on the large and mean size. The Cascade Trail is also crushed gravel, no pavement anywhere, and had a MAJOR WASHOUT, the Skagit river floods multiple times a year most years) that had not been repaired the last time I road it which was two years ago. The first time I rode it the same place was washed out and that was in 1999. Due to the way budget cuts have been I would find it hard to believe it's been fixed. S. Skagit Hwy. on the otherhand is chipsealed but well packed down and in good shape with little traffic, no loose gravel. You can connect with Hwy. 20 just outside Concrete about 1 mile west. Well marked intersection. I just road it this last July on a loop from Burlington through Arlington to Darrington, Concrete and Sedro. No shoulders to speak off but as I said before little traffic, and NO DOGS.
Keep in mind I usually ride a road bike with 700-23 tires. In the winter (wetter weather) when on the old mountain bike I'll use the Cascade Trail, it's also great for jogging and even in some years skiing.
Hope this helps