An excerpt from the interview with the author:
To some people Isotope would look very similar to the work you had previously done with Masonry; can you explain the main differences
between the two?
Isotope has several features that Masonry lacks. Masonry essentially
does one thing, placing item elements in a cascading arrangement.
Isotope has Masonry’s layout logic built in, but in addition, it also
has several other layout modes that can be used to dynamically
position elements. You can even develop your own custom layout mode.
As I’ve mentioned, it has filtering and sorting functionality built
in. Filtering items is as easy as passing in a jQuery selector:
$('#container').isotope({ filter: '.my-selector' });
Isotope takes advantage of the best browser features out there.
Instead of using typical left/top styles positioning, Isotope takes a
progressive enhancement approach and uses CSS transforms if supported
by the browser. This provides for top-notch performance for top-notch
browsers. With hardware acceleration kicking in, animations look silky
smooth on WebKit browsers, and even less-powerful devices using iOS.
CSS transforms perform better with CSS transitions, which I’ll discuss
later.
Another difference is license as @AminAriana pointed out. Masonry is under the MIT license, but Isotope is only free for personal use.
You can buy (25$) Isotope commercial license on this page.