Here are a few design (re-design) preferences I would like to see:

1. When viewing a specific layer, it would be nice that clicking an object within that layer selects that object within that layer and ONLY in that layer.

Currently, clicking on the object sometimes selects the object and other times it selects the object in a layer below (depending on where you click).

I realize that Ctrl-A will select all objects in that layer, but CTRL keys are counter-intuitive. Simply selecting with the mouse is what most people
would try to do by default.

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Hhmm....If you click on an object, and another is selected instead, that means you clicked on the other object. But I understand what you mean. If you don't have the mouse pointer close enough to an object, it won't get selected I think there's a way to change how close you have to be to an object to select it. Let's see if I can find that setting.... Ah-ha! Inkscape Preferences > Mouse > Grab sensitivity. So one option would be to change that -- I think you'll want to increase the number, to be able to select an object from a further distance away. Personally I like a very low value there, so that I have to be right on the object to select it. But fortunately, Inkscape contains many different options for many different workflows

Another idea might be to hide the other layer. And then there's always using Zoom to make it easier to select something when there are many objects close together. Zoom is my favorite for making selection easier