zacmario: thank you for the feedback! I'm working on a stage edit update that will provide a path for the turtles who cant jump as well, though it's tough to avoid giving an easy ledge to attack from. The save feature helps a lot in avoiding getting stuck for the time being, at least.
Glad to hear this is known and being fixed. It was my only significant issue with the hack. I didn't actually end up in the situation where I had only Donatello but it did occur to me while playing that something like that could very easily happen to someone and they shouldn't have to reset just for that.
What about adding ladders to those spots instead of additional ledges? That way Don will still be at a disadvantage as now he has to make himself vulnerable climbing the ladder, but at least then solo Don will technically be completeable.
Also I love up+start for quick-switching of turtles but I'm not so keen on down+start. There are times when I want to pause while crouched (e.g. technodrome hall of death while fighting wave after wave of jetpack guys) but instead I end up insta-changing from one almost-dead turtle to another unexpectedly and get squished.
Otherwise, I absolutely love the hack and I'm glad that serious work is finally being done on this game.