They could given the stage to Sonic but that would be too much of work given the deadline (plus more budget) since Sonic Generations has to be remade instead of just remastered.
The game is basically just Shadow Generations (with the remaster of Sonic Generations as bonus).
They've already made Sunset Heights and Chaos Island for Shadow Generations. They could've just copy-paste Sunset Heights and import Chaos Island to Sonic Generations and modify it for Sonic.
they would just need to work on a stage representing Sonic Lost World then.
Besides, Shadow Generations was the only incentive to buy Sonic Generations along with it. If they were willing to rewrite the script for the game, then they could've added more to it if they wanted to.