Is that it brings fluff into the battles.
We can already have Grey Knights fighting against Imperial Guard, Blood Angels, or even other Grey Knights (go to any tournament and that'll be happening on half the tables), so why the hell does GW think it's important that the Grey Knights leave their Tyranid allies at home?
Everything should be able to freely ally with everything. Making allies accessible based on background is the most annoyingly imbalanced thing GW has done in recent years.
The constuction and capabilities of an army should be based entirely on gameplay balance, not fluff. If a player wants to constrain themself due to fluff, that's their prerogative, not the games designer's.