It makes a massive difference, the game was balanced with 6v6 from the get go, removing a tank completely changes how the game works.
They had problems with certain tank combinations, but instead of addressing that directly, they just removed one. A lot of changes they made just felt like justifications to calling it a 'new game'.
The devs are too proud to add a 6v6 mode along side, it's took so much pressure for them to finally 'experiment' with 6v6, they just won't admit their modes, changes etc are failures.