I prefer SM3 for the obvious reasons.
Sam Raimi is a visionary director (at least when it comes to visuals and camera work) while Story's work looks like a TV movie.
The screenplay and direction of SM3 developed its characters into human beings. There were genuine moments of humanity and real emotion in SM3 and artistic value.
Story's movie is a commerical for action figures. The screenplay services the action set pieces and the sit com one-liners but has only one or two moments of genuine emotion (one between Johnny and Sue at the wedding and the other between Johnny and SS recalling his pasat).
Both disappointed in big villains, but Venom still got 15 minutes of glory and did more in the movie than he did in the comics. Galactus got a whopping 4 minutes as a cloud. Woo-hoo.
But I can see why some prefer FF:ROTSS it is a fun airy movie. As an adaptation it is semi-faithful and it is entertaining enough to enjoy. But it is a mindless summer movie. Fun popcorn but it is vapid and empty.
This includes boring action sequences like the ferris wheel and actions and motivations so stupid it makes the butler scene in SM3 look like a moment out of The Godfather. I am referring to things like the general siding with Dr. Doom, letting Doom walk around with only one guard in his bunker but not the FF, even though he KNOWS Doom has super powers. And Doom having no real reason to get the cosmic powers other than to have them and not caring that by doing so he is dooming the whole damn world around him he wants to rule.
But hey. Also, I wouldn't say FF2 has better pacing. It is shorter, but it has no momentum. It starts and stops with each scene. It maintains no mood or suspense. The only action scene where things feel like they are at stake is the last 2 minutes when Silver Surfer defeats a cloud. The movie just plods along with a sitcom beginning and middle with set pieces in between for the action.
SM3 has rising action and tension as Harry reverts, Peter goes off the deep end, when Venom is born and when Harry comes to rescue Pete. Not to mention the story moves and doesn't sit statically.
Really the only reason I can see you preferring FF2 is that it is mindless spectacle that is easy to just sit at like a sitcom (say Friends, which the first 20 minutes is with superpowers) and as soon as it ends it is in one ear and out the other. Nothing to rememmber.
SM3 was disappointing and had its flaws and faults but Raimi wanted it to stay with you and leave an impact. YOu can argue whether he failed or succeeded until you turn blue, but at least he tried something more than to push action figures.
Oh well.