Welcome to the community
That is one big project you have there. I also think it's doable with Construct 2, but take scaffa 's advice and start some smaller projects to get the feel and hang of Construct 2. Since you'll need to optimize and organize your code well for such big game, prior experience in the engine will be very valuable.
Yes, you can create saves that can be read by other games as well (or other episodes). You'll just have to make a custom save system and save the data into a file.
Also, if you want to code something, you'll use Javascript and not Java since C2 is a HTML5 engine.