Yeah, I think it would have been brilliant if both storylines had gotten a season each as was originally planned. Fuller & co probably knew with a fair amount of certainty that there were never going to be a 4th season, so they incorporated Red Dragon into the 3rd season directly.
Armitage was really good as the Tooth Fairy, and the gay subtext actually became something more than just subtext in the end which was pretty cool. At the same time I feel sorry that they didn't get a chance to explore it more thoroughly. I loved the idea of turning Hannibal into a Shakespearian love tragedy. It might be the first tv show I've seen that has actually canonically approached the domain created by its own fandom's slash fiction. The term "murder husbands" was amazing fan service in that sense.
Agree about the previous works based around Hannibal Lecter too. I'm not a fan of either Manhunter or Silence of the Lambs. I thought Hopkins played the role in Lambs like a fucking pantomime villain and Cox isn't much better (Hopkins obviously copied him for his own 'interpretation'). Manhunter edges it by being an actual cinematic experience though, much of it thanks to Mann and his aesthetics. And Hannibal the film is just a fiasco of epic proportions. The TV show is the best thing anyone has ever done with these characters, and that includes the source material.