I think Katatonia reach a much higher level of emotion and atmosphere than Porcupine Tree do, and therefore rate higher in my mind. PT songs, to me, seem like they exist more as musical experimentation and something to rock out to, rather than something that's meant to have a narrative or emotional journey. The last 2 albums seem more focused on achieving that, but I still don't really feel anything in their music. I just enjoy their songs.
I guess you could say PT push a message along with their music, rather than try to recreate emotions within their music. Despite being pushed as a band that redefine music, they are very much a rock band.
I also think Katatonia do a better job at blending the elements together seamlessly. Probably because Katatonia are a lot more subtle than PT, and pay more attention to the fine details of how various parts of the song run into and/or support eachother.
That and Kata's sound just appeals to me more. Musical tastes is something we will never agree on. I know a lot of people that prefer PT and other music where the elements are much clearer and defined and, well, rock oriented.
Musically I guess they're similar because they both have 'progressive' song structures and merge heavier, rock influenced parts with electronica. But Katatonia have more of a doom metal meets rock and electronic soundscapes thing happening, while PT are pretty much just hard rock and electronica mashed together in long songs with lots of twists and turns.
The similarities pretty much end at "progressive" and "heavy guitars". Porcupine Tree hardly pioneered either of those, and their influences and execution are so different that the comparison is pretty flimsy at best.
it's also worth noting that PT have been becoming gradually heavier and darker. If you really want to make the comparison, I think PT are trying to be more like Katatonia