I for one really enjoyed the boats when they were around and was really sad to see them go. I liked it and didn't think they "sucked" because I knew what they were supposed to be: a water taxi to the other side of the park---and it provided some amazing views of the ToL and the rest of the park.
For some reason (probably mostly because of how Disney marketed the attraction in guide maps and stuff... considering AK opened with very few actual attractions, EVERY attraction they had was considered a must-see.) People misunderstood this water taxi to be some kind of E-ticket must-see attraction and would wait well over an hour for it.
This is what led to the ultimate demise of the river boats. People waited well over an hour for a boat ride that was pretty much the AK equivalent of MK's Railroad ride around the park. While few people would ever consider waiting that long for the railroad at MK, They were doing just that daily at AK, and got off saying "We waited an hour for THAT!?"
From what I hear, before you knew it the boats were one of the most complained about attractions ever and therefore were eventually closed. I also hear the boats are still docked backstage and brought out after park close now and then just to give the water some circulation. Without the boats keeping the water moving, the stagnant river water now provides the perfect place for mosquitos and other things to grow.
I for one would love to see the boats make another return. As has been said, they were relaxing and provided some great views. The fact that the docks are still in place and the boats are still backstage leads me to believe they can/will be brought back some day in the near future. The park is quickly becoming a full day park and has a growing list of attractions, meaning it wouldn't have to depend on/market the boats as a must-see attraction, but rather what they really were/are: a relaxing water taxi to the other side of the park.