SAF had full power at United. Pep never had that at Barcelona. If rumors are to be believed, he did push for some hard squad decisions and a rebuild after his first 4 seasons, as he was dealing to a clear drop in motivation. And he was denied by the board because they didn't want to cut very successful stars.
Ferguson basically ran United while he was there. The ultimate authority on every squad decision probably. Guardiola never had that, which is a unique thing to have as a manager. Obviously, Ferguson had that because he was a great manager, but still, not all top managers get that trust and power in a big club.
The problem at Barca is that the club is highly politicized. Every board will want to make their own decision and promote their own ideas, and because of this managers don't have much continuity. It's no doubt probably that Guardiola was seen as Laporta's guy.