In X4 many (most, maybe all) of the tools like the flood fill and airbrush tools now work with 16 bit files. In previous versions the program to convert the file to an 8 bit file. That's why a gradient mask would result in banding. Now the tools work with 16 bit files. So the 16 bit support is a major thing, for me anyways. Plug-ins support 16 bit files as well, or at least the plug-ins that are 16 bit compatible.
Most layers are the same. They added 3 layers, but I don't know if they'd do you any good.
I don't think anything has improved in the aligning pairs front I'm afraid. Could be wrong.
Cloning and healing, much the same, except they now support 16 bit files unlike before.
For me, color management is poorer, I don't have Adobe RGB for example, but I think I'm an exception. The program should support that and a few other color spaces.
Actually you just made me do a comparison to a file I had on my computer. I checked the Color Balance correction tool and I've gotta say I've been unimpressed with previous versions of PSP, but X4 seems to make a pixel white when I click on it. Preliminarily I'd say that color correction is improved.
Just personal observances here.
"Smoke me a kipper, I'll be back for breakfast."