I dont think that one particular thing or another is the cause about one movie is bad or good. I mean, the organics were a crappy idea, but there are tons of more factors being the cause because the spiderman movies sucked so bad.
Iron man was a far better movie not because one particular thing , because a lot of things.
By the way, i loved iron man , i think that it captured the spirit of the comic very well and the story and the characters were pretty good, except the weak end climax and some plot holes. I loved Downey jnr was Tony Stark, i think that he was almost as good as christopher reeve as superman and christian bale as batman, probably the two best comic chararacters performances.
In the other hand, Indiana Jones was a dissappointment. The original triology was pretty good, this one sucked and you couldnt feel the same tone of the other ones. Plus, the script was terrible and the performances weak, specially great actors like John hurt or Cate Blanchett.