I haven't paddled the Allagash but I've paddled a lot of big lakes and rivers in my time.
If you get nervous in the shallow Independence (11.75") in big waves and wind on big lakes -- and that sure happens in northern Maine -- then that, I think, would answer the question for me.
With a lot of gear, you won't have much freeboard in the Independence, whereas you will in the 14" deep Alaskan.
Psychological comfort often outweighs the physical performance of a hull, most particularly when you're out there all by yourself in the wilderness.
Plus, you don't have to do much maneuvering in big lakes and rivers. I don't have personal experience with Chase Rapids, but most big river 2's aren't usually particularly technical, and certainly canoeists have been running it in tandems since the memory of man runneth not to the contrary.
Canoe / Kayak Anchors
Touring Kayak Paddles
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