First off, I think they WILL kill off Mary Jane (ala Gwen Stacy). Tobey Maguire has stated before that he will stick with these films as long as they will have him, and I imagine he'll keep that promise as long as they take breaks and allow him to do a few other films on the side (like they are right now basically). Kirsten Dunst has basically stated that Spider-Man 3 will be her last. That means they'll either kill her or recast. I think Raimi will go for the former, and then bring in Black Cat on down the line, as they have considered off and on for awhile now. This works in many ways. If Harry ends up being the cause of it, then it will finally drive a permanent wedge between the two and set us up for a huge clash. It will also cause more hatred between Parker and John Jameson for use later on, be it in the form of Man-Wolf or Venom.
Three more films beyond the upcoming one will also allow for a slow build-up to Venom as well, which is what we really need for that character to work. Villains for 4 & 5? You already have The Lizard set up. You could also bring in Mysterio or Kraven or the Vulture if you wished, leaving Venom as the villain for Spider-Man 6. I don't think we'll see Carnage though, especially if Raimi sticks with the series. We all know that Raimi is not too fond of the character, but Venom's popularity is so great that if they continue with the films past Spidey 3, there's no way that they'll get away without using him. Carnage, however, is just a Venom knockoff. If Raimi doesn't like Venom, there's no way he could like Carnage. If they bring in Carnage, they need to allow Venom his own film first though. Whoever for 4, Venom for 5, and Venom & Carnage for 6. I still maintain that Carnage won't make the leap to film though. When all is said and done, I'd imagine the saga would play out similar to this...
Spider-Man = Green Goblin, Peter graduates, Peter falls in love, a hero is born.
Spider-Man 2 = Dr. Octopus, Peter struggles with keeping dual lives, atonement, and love is cemented.
Spider-Man 3 = Sandman, Harry takes on the Goblin mantle, dealing with the loss of a loved one (Mary Jane).
Spider-Man 4 = The Lizard and Black Cat, new love interest, entering the work force, Eddie Brock and the new suit are introduced.
Spider-Man 5 = Villains? Problems with suit, various life problems and issues, Brock is fired.
Spider-Man 6 = Venom and various life problems.
There is a lot of foreshawdowing in the final scenes of Spider-Man 2, especially the funeral bell-esque sound during that final shot of Mary Jane. Raimi is using the story to portray the problems and issues of entering adulthood and the sacrifices and heartbreak that one must always endure eventually. Everyone loses a close friend at some point in their lives and I'm sure this will factor into the series storyline somewhere. Couple that with the foreshadowing of that final shot in Spidey 2, and that Kirsten Dunst has stated a desire to leave the series after 3, and you can see what it probably adds up to. I think we are in store for a delayed Gwen Stacy scenerio. Peter vs. Harry, and Mary Jane will be killed in the crossfire.
Is any of that right? I imagine some of it is, but only Raimi himself truly knows. Even if he doesn't stick around for all six, I can see him at least helping to lay the groundwork for those installments. I'm guessing that if he isn't burnt out after Spider-Man 3, there's going to be break of a couple of years while everyone does their own thing (Evil Dead 4 maybe?). I couldn't picture any of those involved wanting to head straight out of one Spider-Man trilogy and into another.