I wouldn't change too much.
What does surprise me about the islands is how much of it is inaccessible. There's the private yacht club, and some huge swaths of land towards the island's west side that are taken up with water filtration, something to do with a lot of radio masts, and basically just blocked off.
Right now, when you land at Centre Island, to get to Hanlan's point, you have to meander north-east all the way to the back centre of the island, then walk in a curve around the south end to get to Hanlan's point. There's basically only one path, and it's a long walk - especially if you're trying to catch a ferry,
In my plan, first, an entirely picturesque canal would be dug between the island airport and Hanlan's point. It would have a little inlet that opened onto the Main canal, too. This would psychologically and aesthetically separate the islands from the airport a bit. The Island Airport would somewhat cease to be part of the 'islands'. Tunnel to the airport? No big whoop!
It would divide Hanlan's point slightly in two, but that's just another opportunity for a scenic bridge giving a romantic view back up the main channel towards the Centre Island bridge, along the racecourse.
Maybe there could be a little bridge over to the remaindered part of the beach - which might help sorting the naked from the nude.
More importantly, two paths would be put westward from Centre Island to Hanlan's point. One would go right from the ferry dock and meander over a few bridges to get there. The other would go diagonally from about where the school is located now, and traverse through what is now largely inaccessible "mystery land". (Paths shown in pink and yellow). Although the city (and dock owners) might be reluctant to part with the land, if the width of the paths were kept narrow, surely they could be accomodated with minimal fuss? At best, a big part of lovely nature might be made accessible on the south side of the main channel.
I also put a little dock in this proposal for a little summertime shuttle to Ontario Place. That would be fun. Not to mention one to Cherry Beach and the Tommy Thompson Park lighthouse. It could be located at the Centre Island Pier, and free for anyone leaving the island.
I also think the island needs some seriously good restaurants and bars. The overpriced and soulless food currently offered there is no thrill.