I agree with you that the album's length is a large part of what keeps it from "flowing," though of course as a rabid fan I'm thrilled to have all the tracks, especially considering Mac's current pace of one new album a decade.
Another problem is the inclusion of the kind of self-indulgent tunes that really belong on solo albums ("Come," "Murrow," "Silver Girl," "RTTG"). As fun as "Everybody Finds Out" is, I think it will sound dated very quickly, while "Smile at You" falls prey to Lindsey's overproduction. Cut those out, along with the unnecessary retread of "Bleed to Love Her," and you've got an album that's solid all the way through.
I wouldn't add any Christine tracks, though. As much as I miss her, she just wasn't a part of this project, so I think it would feel forced to include her "Time" songs.
Here's my 11-song version of SYW:
1. What's The World Coming To
2. Thrown Down
3. Miranda
4. Peacekeeper
5. Say You Will
6. Destiny Rules
7. Say Goodbye
8. Steal Your Heart Away
9. Illume
10. Red Rover
11. Goodbye Baby
(I broke up the pairing of "Say Goodbye" and "Goodbye Baby," which I found a little cutesy.)