Sorry, I'm late to the party, and I haven't read all of the replies. I'll go back and read this evening.
Don't be upset if you get a little resistance to your ideas. Thinking men debate all the time, and the result is often a thoroughly thought-out end product.
Stay cool, and don't feel threatened or offended. Listen to everyone. There is a huge amount of experience and knowledge here, so chew on suggestions before accepting or discarding. Once you decide on a course of action, the folks here will respect it and will try to help you reach your goals in the smartest way possible.
Like you, I recently got a 16' boat for cheap. It was a "fish and ski" type, and I didn't like the layout of the boat. I put it up here for discussion, and I got a lot of suggestions. Some I liked, some I didn't. But folks helped me think it out carefully before making any final decisions.
What I ended up doing was make the entire front into a single platform, and I also put a small platform in the back with a small splash well. I am very happy with the end result. Here is a picture of it during the "test and see" process:
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It took a bit of work and material to reinforce the transom area properly, but well worth the effort. That little platform gave me rigidity, a place to cast from, comfortable seating, and it made it much easier to get in and out of the boat with the ladder that isn't in the picture. This was important, since we swim and tube in the summer.
Here are a few more pictures. Since then, I've refined things, and I still have more to do in time:
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But enough about my boat, on to your boat...
I had a Starcraft last year with the same rear area as yours. As you state, it takes up a LOT of real estate. And, as stated by others, it is a structural part of the boat, so it will take some careful planning to re-engineer it to be both strong and safe, but it can be done.
Are you comfortable with installing solid rivets? Do you have a MIG or TIG welder that you are comfortable using on aluminum? Do you have a metal break (bender) at your disposal?
With the right tools, you should be able to do some nice stuff.