A few thoughts:
- One can stay longer than the ferry schedule dictates, just look for the next ferry to the next town;
- (having been in both places) I'd recommend going to Sitka and spending longer than currently shown in Ketchikan.
- One can get to Southcentral (vs. just Southeast) Alaska by taking the AMHS to either Valdez or Whittier....you're then on the road system and can go to Los Anchorage, Kenai, Homer, Fairbanks, etc.
- Out of the way, but might consider running across the Gulf to Kodiak....