They had to have another villain in this for Peter to fight aside from Harry: Harry could never be the central villain for commercial reasons, the Goblin had already been done and the studio wanted someone new.
It couldn't be Venom either, because if you're doing the symbiote storyline Venom only happens after Peter loses the symbiote.
Also, they had to have Peter going bad before he got the suit and the suit only amplifies what he's already feeling. If they gave us Dark Spider-Man as a direct result of the suit the general audience would complain that Raimi used the symbiote as a plot device to give us a "Dark" Peter instead of having him go bad on his owna nd the darkness be a truer part of the story. Having the suit be responsible worked in the cartoon because it was a cartoon. It wouldn't work on a big-screen version.
Therefore, this new villain had to have done something to Peter so awful it would make him want to kill him even before he got the symbiote, and only killing someone he loved would do that. They couldn't get rid of MJ or May so they had to tie this villain to soeone Peter loved that was dead. Ben was the only choice.
And since they thought this was the last film, they had to not only introduce all the amjor players but WRAP THEM UP as well, this includes Venom.
Probably for the best they did use Venom in this. If they hadn't and then someone else later did the Venom story the audience would be all "why are they doing another Dark Peter story? They did it before and he didn't need this alien goo as a plot device to go bad, it was his own inner demons. And he beat them so why is this happening again?" It would rob the symbiote of its potency.