I agree, 3.5 hrs in a 737 at the end of a long trip is not something I would eagerly anticipate.

But you don't have to do an overnight say if you want. You could take the 7:12 AM flight out of JNU, stop in Ketchkan, then transfer in SEA and AMS. It's an extra stop but no extra transfer. Depends on your preference for an overnight stay or not. If you wait another 2:10 in AMS you can take SU in a 320, but I guess that's not much different than KL in a 737.

Too bad that there's not a SU flight out of ANC.