Eh, I don’t think it’s the same thing. The gulf between “photos user” and “pixelmator” user is quite high, much more so than “weather app” and “weather app but better”.
In particular, if you have the average user Pixelmator, they’d be worse off. The same isn’t really true with weather or darksky - they really just do the same thing.
We still have iMovie and FinalCut, GarageBand and Logic. Apple has kept two different product lines before.
Also remember that some of those have been crippled in the past. iMovie used to be way more advanced. Older versions of Pages had (pretty basic but still) layout options that were completely removed.
It's also not impossible that Apple moves a few of Pixelmator's tools into Photos but kills the rest of it, either actively or just by stagnant development.
In particular, if you have the average user Pixelmator, they’d be worse off. The same isn’t really true with weather or darksky - they really just do the same thing.
We still have iMovie and FinalCut, GarageBand and Logic. Apple has kept two different product lines before.