Well you kind of summed up where it is at. We’re all pleased with the current feature set. It was designed around a premise, and we put as much toward that premise as we could, without too much, and called it good. This isn’t the type of idea that needs continual development. Periodic development, absolutely, and that will happen, but for us all to be sitting around day in and day out doing nothing but thinking about Scapple would get pretty boring after a bit! There just isn’t that much that needs to be added or changed about the core idea. Refined, evolved over a period of time, sure, but it’s already doing what it needs to do.
I wasn’t sure if this was a complaint, because we consider that a feature, both for the search indexing as you mention, and the fact that anyone with a little XML knowledge can take advantage of that, as well as third-party programmers who are interested in working with the format. It’s a philosophy we take with Scrivener as well. The whole format is wide open and already other developers have taken advantage of that, integrating tools with it.
As for the rest, I think you just need to dig a little deeper, we already handle the things you’re asking for.
Have a look at the style sub-menu in Format, you can do all of these things you are asking for already. The default styles that ship with the program are just examples. We’re glad if you find them useful, but please make your own too. You can even create your own defaults and override ours entirely. Check up §6.3 (pg. 47 on) in the user manual PDF for details.
That should be possible, but since not every program copies images the same way, you may sometimes have to drag it in as a file, too. Either way you can get the image there where you need it. I just right-click copied a graphic out of Firefox and pasted it into Scapple without any fuss.
Already possible as well: just select the text you wish to link, use Edit/Add Link… and drag and drop the file you wish to link to into the URL box. Now you have a clickable link to another .scap, or any type of file or Internet address for that matter.