28 more scenic, 31 faster. Just my .02. I do 28 90% of the time in, 31 50% of the time out. This is one of those "what's better: chocolate or vanilla?" things
If I am coming from the south I take exit 28, if I am coming from the north I take exit 31. One more bit of information for you, 49 is paved Tripoli is not.
I ususally go via exit 31. It's roughly 7 miles from I-93 to the trailhead, which is at the height of land. On busy days the lot fills up and you have to park along the road.
Which way, depends on when I go. On a weekday not during peak camping season or on a weekend when I'm there before 6:30 AM or leaf peeping season, I go via Exit 31 as I'll drive faster on the highway where I can pass people & then faster then the posted speed on Tripoli. (When campers are awake & moving around, you need to be more careful.)
If you drive the posted speed limits, it's probably quicker via Waterville.