I did a simple test for all three by importing a frame I'd been working on and doing, in order: layer manipulation (increase opacity of sketch, make a new painting layer between the linework and the base color); eyedrop the shade color in sketch; make a rectangular selection to paint into; paint in another selection trying to make the two sides symmetrical; freehand paint the rest of the details. This somehow took all day because I kept getting desperately tired/ eye strained from the UI differences. It probably says something that by far I farthest I got in one sitting was with Clip.
Importing: All three were able to import properly...once I reconverted my general pdfs to PSD. Weird. Krita takes longer because it wants to default lower the resolution and I have to manually type the original l, w and res.
Layers: Sai, Clip tell you layer opacity at a glance, which I didn't even know I wanted (I use opacity in nearly every document but can lose those layers). I don't like Sai's "linework layer" nonsense and how the tools are restricted to different layer types but I didn't have much time to play with it.
Selection: is more comfortable to use in all three, most comfortable in Clip where the selection is moved on drag by default (rather than artwork). It has a nifty UI directly under the selection for easy deselecting (!), crop, deletion, copying, and deleting the rest of the layer, but inexplicably moving the selection is only in main sidebar.
Shortcuts:
None of them have PS' Shift (make straight 180 degree or 90 degree lines)!! Clip and Krita can achieve it with the line tool, but Sai's line tool is stupid and prohibitive so far. Google didn't help.
I have to manually make 'Z' the zoom tool, but that's fine
Layout:
Sai's is the most sensible. For the dropdowns, I like how straightforward the categories are and how the shortcut is given. I like the layer transform options under 'L' and easy canvas flipping under 'C' (in the sense that the options aren't buried in further menus).
On the other hand, CLIP IS THE ONLY ONE WITH A HISTORY WINDOW! History windows are much faster than ctrl+Z for undoing drawing when used to having them. Clip is the highest fidelity to the PS layout almost to a fault, because combined with its additional features its dropdown menus are difficult to parse and not awfully useful yet save for selection.
Oh, I really like that Clip's gradient UI takes after Illustrator rather than PS (but improved over both). A lot more flexible.
I really, really like Krita's middle of the road between ease of use and familiarity, but I don't have any clue what color I'm using most of the time. It wasn't at all clear that the tiny swatches in the top are gradients rather than my functioning color.