On the controversy scale, Figo's transfer to Real Madrid tops is the highest IMO. All the ingredients for a controversial transfer were there (Real-Barca rivalry, Figo being the best player for his club and country and one of the best in the world, the release clause that Real activated but Figo didn't seem that enthused to join Real but was forced into eventually as he'd have had to pay Florentino Perez alot of money for not doing so) and only thing that would top it would be Messi joining Real Madrid, which won't happen.
Neymar's transfer was a shock but not controversial as it was inevitable with the rise in transfer fees that A club prodigiously financed would pay a ridiculous amount of money for a player. Had Neymar joined Real Madrid for that amount, then yes.
I'd suggest the Tevez-Mascherano transfer to West Ham and the punishments and the consequences would be high on the list for controversial transfers involving an English club.