Alright, I've been pixelling a lot lately so new thoughts are coming to me. It's refreshing that stuff so elemental as what I'm about to suggest hadn't occurred to me. It means there's a lot more work to do to become better.
So, stop pencilling with a freehand dot. Use the line tool instead.
To qualify this, I am not talking about rough flat concepting, I would suggest freehand for that and a not-single pixel brush. Go from general to specific. But when you start rendering, essentially whenever you go to a single dot pixel, avoid working with the freehand tool, use the line tool (I am assuming the line tool is showing you the preview of the line you're drawing before you let go of the mouse button, a la Pro Motion - I don't think there's any pixel app that doesn't, but it's important so I'm mentioning that too).
Here's why: When you work with the freehand dot you tend to create bad, jagged clusters which you then clean up. That's fine, but I am sensing it puts the mind in a bad place to start with messy shapes and move to cleaner shapes *when rendering* (in concept flats, it's impossible to not have to do this). Make an effort to switch mindsets by switching the tool, and only put down clusters that have good shape when rendering.
The line tool helps in this because you can see a shape in front of you and you can alter it before you let it 'fall down' on the paper. Freehand doesn't do this, you can only undo. Getting caught in an undo-loop is bad for obvious reasons. So try to be mindful when you put down lines, even if they're 2-3 pixel lines. Consider perfect angles, and try to think ahead "how much of this cluster am I going to paint over when I go to a darker/lighter colour?'. In that in-between stage where you're rendering over flats, but not doing final nitpicks and hue shifts and other fancy stuff, try to describe the bulk of the information in the thing you're drawing with that middle shade, so when you paint over with other colors, the cluster guide is right there in the middle and it's a matter of replacement of parts, tapering edges, making an edge softer etc, than it is to add additional clusters that override older clusters. That's when you're left with ugly single pixels and odd jumps in the palette next to each other in unflattering ways.
The line tool helps visualize a good shape before you put it on the paper. It seems like a simple idea, doesn't it?