I'd probably use selection tools sometimes. But MasonMac, for your two issues so far, here are workarounds:
The bucket is actually pretty good IF you use hard pixel brushes (at least for the inside of the area you want to bucket fill). You can make a new layer (or copy a layer) and use that to paint up regions to bucket. (That said, bucket filling I often do in another program most of the time -- my workflow is sketch in mypaint, flatten in other apps, color in mypaint.)
And for wanting to move something but it's in the same layer as something else good: copy the layer! in one layer, erase the good thing, in the other layer, erase everything except tthe good thing.
All of that said, if you want to love MyPaint you sooner or later have got to get comfortable with using other tools. It sucks that GIMP's ora support is so lacking. But. Usually you can do what you want to do with a little work and ingenuity.
Honestly... I agree actually, that selection tools would be useful. One thing I use a LOT in MyPaint is this construct: a layer group with two layers. The top layer in the group uses Destination In, the bottom layer is normal. And then I paint on the bottom layer. The top layer is sort of the "selection". I set this up via scripts (doing it manually like PeterToybulldog does, that's unreasonable since I often have twenty, thirty layer groups like this). But... it's still cumbersome.
I usually use svg layers for these top "mask" layers, and a paintable raster layer for the bottom "paint" layer in each group. For example I might make a hand outline in Inkscape, put it as the "mask" (Destination In) layer, and then I can paint the hand underneath it on the "paint" raster layer.
But setting it up by hand, setting the blend modes, creating the masks etc, that's such a hassle compared to Manga Studio where you can just have a flatted image, select with wand on a selection layer and then paint within that selection (a la Destination In) on a paint layer.
Since I use MyPaint, I have scripts that set up these "Destination In" layer groups to "emulate" saved selections. Generating the ora files. But, they become big and slow.