Rafa needs more control.
The main thing irking him is the Academy setup, Piet Hamberg was brought in, but apparently he does not get on well with the other youth coaches. Rafa want's control over the academy so he can decide what youngsters are bought in, as of now he has no say in what youngsters are signed, only a say in whether or not they can be moved into the reserves.
SA and AW have complete control of their transfers. Peter Hill-Wood has mentioned many a time that Arsenal have £30m to spend on whoever Wenger chooses but Arsene chooses not to spend. SA identifies his target - budget allowing and Gill goes off and does whatever possible to get that player.
Rafa on the other hand tells Parry who he wants, for e.g. Dani Alves, we have a budget of £15m. Rafa of course would push to make sure that he could get Alves at whatever cost upto £15m. Parry on the other hand thinks we could save some money here and keep a bit of our budget, we'll only bid £7m. Seville wanted £12m, the most Parry wants to pay is £10m despite the fact we have a budget of £15m and this is the only signing Rafa wants. Another example has to be Cristiano Ronaldo, Liverpool baulked at the £7.5m quoted price after scouting him for months, Gill heads out to Portugal on the instruction of SA who having seen Ronaldo playing at firsthand in a friendly a week or two previously and pays £12m, what Sporting wanted, and get's the player. (Obviously we hate the c*nt, I'm sure it would be different if he played for us though and we would have loved the fact he got Rooney sent off)
See the difference? SA and AW have total control over their budgets and their academies, they don't have a Director of Football at their club. Whilst here Rafa has an idiot who thinks he's a DoF as well.