Thanks, setha, glad to hear the program works well with how you record thoughts. Some of these ideas aren’t bad, but they would require a lot of programming—more than would be reasonable to expect from a $15 tool. But even beyond that, I think it really boils down to the goal of Scapple. We have plenty of programs out there with hundreds of features and a ton of flexibility for visualising concepts. The problem is, you can’t really use any of them at the speed of thought, and a major component of that failure is in just how much control you have over every detail. Scapple is meant to be an answer to that problem, so adding these things back in sacrifices its intent.
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Bezier controlled curves for example are not something that can be easily programmed—and when the point of the software is to just slam down a bunch of raw ideas quickly and without ado, something like fiddling with the precise curvature algorithm with an assortment of handles is a bit outside of its scope. There are other ways to resolve confusing line overlaps on an infinite canvas. There are other theoretical problems with precision line adjustment, like the loss of agility in a program that is all about agility. Scapple lets you rapidly expand and contract ideas and move things around. If your lines are all carefully manicured around other notes and other lines, you will become mentally burdened by the arrangement. Keeping connections raw and simple means you do not become attached to the arrangement and feel liberated to radically remodel as you go. This is, we believe, a psychologically important component to thought capture. Our brains do not produce linear perfection. We start, halt, revise, recurse, blunder and then finally say A-ha! We need software that doesn’t shackle us to each of those phases.
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Likewise, precision placement of where the line intersects with the note—not a bad idea, but is it worth spending all of that time on (and I speak for both the programming involved and all of the users dragging little nodes around pixel by pixel), when all we really need to be saying here is “Note A <-> Note B”? Scapple is about keeping things concise and to the point. But incidentally you can toggle between drawing to the centre of the note, or to the nearest edge, in the “Document” tab of the inspector. That is more of a global preference though, at least for that document.
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This can already be done. Hold down the Spacebar and then click and drag.
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You might try approaching your boards in a different fashion if there are that many overlapping lines, and remember that lines are the emphasis, not the bread and butter. Just placing eight notes near to one another “says” something about them. They do not need a complex of lines between them to underscore what is already being said spatially. That is one of the differences between Scapple and stricter mind-mapping or purist concept-mapping software, where visual links between nodes are of utmost importance to the structure of the idea.
That aside, this has been requested before and denied by Keith, so it is not likely to appear. I myself do not think that highlighting the link lines of selected notes would harm the philosophy of the software—but I do question the necessity of such a feature given the above. I have used programs that feature this, like Tinderbox, but they are for much more complicated modelling than Scapple is, so it’s not easy to say that because it has been done there, it should be done here too.
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This already basically exists. Instead of having some external widget you click around in, the entire board is already a navigator. Depress and hold the Z key to see your entire board, point with the mouse where you want to move your view, and let go of the key. Better than a navigator widget, you can actually do mouse-based editing while the Z key is down; great for moving a cluster all the way across a large board.
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That could potentially come in time, but it wasn’t a priority since rich text editing inside of notes is a bit out of scope. We do have a system in place for inline formatting like bold and italics, though we don’t want the format to be burdened with complicated formatting syntax. Right now the .scap XML format is pristine, increasing its utility and transparency.
I’ve used 3-D mapping / outlining / mind-mapping software before, and in my opinion it’s one of those things that looks better on film, with Hugh Jackman clapping and drinking wine in front of six monitors as he “hacks”, than in reality. 
Controlling a simulation of three-dimensional space on a 2-dimensional surface with a single-point modifier alternated control is far from intuitive and easy to master. Even with a multi-point control it’s just awkward and gimmicky in my opinion. I tried out a 3-d outliner on the iPad once—it was fun but it took ten times as long to anything I wanted to do.
But controls aside, that really oversteps the cheap-and-simple-tool philosophy for a program that stays out of your way and lets you jot down a quick idea without having to think about technology while doing so.