There was often thousands of empty seats (and areas of space on the terraces) at MR until the Kippax was re-developed, most seem to forget that. Even if you could take off the current empty seats, our attendances are at record levels.
The current atmosphere isn't helped by the negativity about the team, and people getting on the backs of certain players when ever they make a mistake (this has always been the case, but seems worse at the moment), its not just down to the empty seats though it doesn't help.
Despite the best of intentions, the new singing section isn't working for me, because anyone that's not in it, can hardly hear it, so other songs are started, particularly in SSL3. SSL3 has had some good atmosphere at times, but not always, it was pretty embarrasing for instance against Liverpool, when people were leaving before half time. If it was up to me, I'd try and relocate all the singers up there, the noise is good with the roof above, and it carries elsewhere, the trouble is for cup games, everyone will be scattered round the stadium again.