My reading of the situation is that the government has decided that it would be unacceptable to simply let the leases expire. The idea that the cottage leases should be allowed to expire dates back to the 50's which was a time when a cabin in Algonquin had little market value and undeveloped water front property could be still be acquired on lakes outside of Algonquin for a relatively low cost. If leases were allowed to expire it would now represent a significant financial loss to the lease holder and the availability of anything similar within Southern Ontario would be quite limited. The new leases give the government a "Right of First Refusal" when a property is sold so it has the option to purchase and demolish cabins. The trend of placing further restrictions on lease holders continues and rents can be adjusted upwards during the lease if the market value of the properties increases.
The documents from the ministry don't elaborate on how much the rent is being increased under the extended leases. Anecdotally, an acquaintance of my wife told us the annual rent on their family lease was rising significantly and he didn't think they would be able to afford to keep the property. It sounds like Algonquin will go the way of the Muskokas where only wealthy people can afford to own property and people of average means who may have a cabin that has been in their family for generations will be forced to sell.
It's anyone's guess as to whether or not the ministry will actually use their "Right of First Refusal" to eliminate some leases.