Rafa didn't win a trophy for 4 years with the best midfielder in the world, one of most feared strikers in the world (at the time), the best DM in the world, a world class CM in Alonso, a underrated RB and two great CBs in Carra and Hyypia. So yes, they'd beat today's team but they couldn't get it done when it counted in ANY tournament. I'd much rather win 2 trophies after 6 years of nothing, and build on that than finish 2nd.
That 2nd place finish only gave United more of an edge, as per Fergie, "That was the best chance they'll get for the league and they blew it."