Yes indeed I think skin independend functions should be implemented in the jAlbum core.
But the fixed-ratio filter is already very old and has been implemented in almost all skins, so there is no immediate need to move it to the core now.
I think there are first more important things to do.

Personally I never open the Effects panel and I wonder how many users are familiar with that panel. So I would not serach it there.
I thought that the Effects panel was for the slides!

For me there is only one place were you should place this, in the panel where you define the thumbnails dimensions. In my own skin I have these two options now on a thumbnails tab.

Sorry I brought it up. As I think about it, adding these choices to the core would make a mess of things. To avoid conflicts, new skin versions would be needed immediately - otherwise, what would a skin do if the user chose "fixed shape" in the core, but didn't choose "fixed shape" in the skin settings? And a non-updated skin wouldn't even know that it needed to check the core setting, which would produce a hell of a mess.

Tough to explain, but something like the justified gallery of thumbnails really doesn't behave well with fixed-shape thumbs. You end up with a lot of seemingly small, but very noticeable, 1- and 2- pixel alignment errors. So the skin really needs to know what it's being fed, and use very different coding for the thumbnail layout if fixed-shape thumbnails are coming its way.

Even after updating, older skin versions would be incompatible with the new jAlbum, and the new skin versions would be incompatible with the older jAlbum. The fixed-shape option is, indeed, in almost every current skin - even Neptune will add it in the next release (ready to go, but I'm tinkering with some other things).

But if these filters were added to the core settings, the thumbnail bounds panel would be the place for them. These aren't fancy "effects" that get added to the images - they're closely tied to the bounding dimensions. And I, too, think of "effects" as something for slides.