Interesting thread, as they are apples and oranges in so many ways. But comparing what you can, I think what Indurain accomplished, and was as an overall cyclist, is more admirable. His two Giro-Tour doubles still remains very impressive. The only Tour he was pushed at all was 1993 by Rominger, but he still won with aplomb. Mig is also one of the most modest, gracious champions I can recall. Never boasting about any of his wins, he let his riding do his talking, smiled for cameras and signed autographs for fans. When he came to Atlanta for the Olympics, even though his English was poor he greeted as many fans he could.
On the negative side for Mig, the Tours during his years had triple the TT distances that the GTs do today. Not his fault though, but it did work to his advantage. He was also bland to watch. He'd crush everyone in the TT's, and then follow the right breaks in the mountains and rarely attacked with them. Though if you watch a few stages, such as with Rominger in '93, and the amazing ride up the Hautecam with LeBlanc in '94, he could climb at a very high level if he needed to, and probably could have won just about any race he wanted if he set his mind on it. I also recall Mig having the gods smile upon him, as he rarely if ever crashed his entire career, and if he did they were minor spills. Probably Karma for being such a classy champion.
Berti is more of a pure climber who can explode in the mountains like no other and control the race with his will and talent. He is the most feared rider today. He may indeed top either Armstrong or Mig's GT wins, and he really showed the heart of a champion in this year's Tour. He still has probably 5 more years left of racing at the highest level I think, and that will probably be a better time to compare him to greats of the past.
As an aside - This thread is about these two riders, not about doping or Armstrong, so let's keep the discussion on track, please.