At this stage of development, I'm taking the perspective that a novelist might take with their book--it is a "first draft" and I'm weighing getting my ideas down more than polish.
The run-and-aim mechanic was very much reactionary. In the original version, in order to shoot at the boss, I had to come to a complete stop. It takes 3 frames to come to a stop, and in that time the boss could easily get a shot or two in. If I'm getting frustrated with the controls then it's not a good sign
One thing I didn't think to try yet is to beat all of the levels with the minimum possible score, and see how far that gets me. I might need to revise the first level's skills a bit, now that I think about it.
Algebra is a good example-- you need algebra to see the dots when aiming. At first, I thought the dots were more of a luxury, and I wanted Algebra to be meaningful. Now that I have more direction with this game, I realize there are two shortcomings: The dots are more important than first thought (especially for the axe that fires in an arc), and the axes are needed in the first level to kill the turrets. Even if they're doing very well, the player won't have many points in the first level because the majority of points come from style bonuses at the end of the level.
Getting to a score of 1,000 by the time you get to the room with the Algebra book is much easier, so it makes sense to drop the cost. There's probably dozens of these kinds of scenarios that I'll just have to play in different ways to figure out--and, eventually, watch other people play.
If you replay a level, I am planning some cosmetic differences. Substantial changes are rarer, but I do like the idea of having options. If nothing else, that would add some replayability, too. Unfortunately, I can see this making level design much more complicated--but I think it's a good thing to shoot for, and adding new paths in existing levels wouldn't be too difficult once I get one path balanced.
Indiana Jones and the Fate of Atlantis had three entirely different paths. I think something of that scope would beyond what I could do--but the idea of having three variations of the same game is a good one.