I have never understood why this system is so little used it is my favourite cruising ground. NY State could use some marketing help. Most of my Canadian friends don't even know it's here. 2000 kilometers of beautiful little towns, fascinating small town museums, entertainment or some kind of festival every weekend, free docking ( couple of spots will charge $5), free wifi. many spots with free power, some spots with free laundry facilities, free or $200 pumpouts, the list goes on.
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Methinks perchance you're missing one of these, "."
As to the reasons for it's moderate use.
1. Outside of major boat population areas, even the ICW is not really that heavily used, although more so than the NY Canals.
2. Seasonal. It's a lot more difficult to have a profitable ice cream shop in the Northeast too. At the best your usage is going to be only 40% or so that you'd have in a warmer year round boating climate.
3. Not conducive to weekend escapes, but only to longer slower excursions. This narrows down the demographics of the boaters considerably. Most people don't have the time to enjoy the Canals.
4. Slow, lots of locks. This is demographics of customer again. This pace isn't for a large group of people, especially younger and this item is somewhat related to the point above.
5. By many it is not seen as a destination but as a means to get somewhere only. In fact, many who start out seeing it only as somewhere to pass through find it far more to their liking than they expected. Then tying to this, it is an area you have to seasonally clear. If I'm looping, I hit it as soon as it opens up late spring and I am on a bit of a schedule needing to clear Chicago and head south in that same season.
6. Very little local cruising as the towns along the Canals are all small.
None of this is to detract from the great area it can be, just simply to answer your question.
Recreation and entertainment is seldom self supporting. I do agree they could do some things marketing wise to build the popularity some, but not a lot. In fact, building it's use isn't going to really impact the losses significantly. It would take commercial traffic for that and it can't be a shipping route. If anything, adding traffic would simply require more resources to manage it.
Some things we have to decide whether to value for their intangible values. City parks, national parks. Even the arts.