(1) McCain is indelibly linked with the Bush Administration on Iraq, and he is indelibly linked with the Bush economy. On the [former], the campaign points out that McCain long ago criticized the way the war was run; that is an academic point (arguably, a true point) in a world of perceptions. (On the economy, McCain had the chance to forcefully separate himself from President Bush, and he chose not to. He is responsible for this part of the problem, to the extent that it's a problem.)(2) Since 2005, independents have been voting Democratic, have been identifying as Democrats, and have grown incredibly resistant to the Republican brand. That's not John McCain's fault. There is little he can do.
(3) The Democratic party's 50-state nomination process has turned out to be a boon for the party in so many ways; millions of Democrats and independents have already practiced voting for the Democratic candidate; hundreds of state and local parties have benefited financially and existentially from the competitive presidential race; activists are spirited and enthusiastic.
(4) Republican voter registration efforts are tapped out; in 2003 and 2004, the Bush campaign's enormously successful voter registration drive essentially registered a large portion of the remaining soft Republicans in the country. The Democratic voter registration efforts are just beginning; the Obama campaign managed to register 200,000 Democrats in Pennsylvania alone; it intends to register a half a million African Americans in Georgia; millions of young Democrats in the South and West; even if the McCain campaign wanted to expand the pool, the zoning laws of the political universe are controlled by the other party.
(5) There has been, and there will always be, tension and mistrust between McCain's world and the Republican establishment.
(6) Rick Davis and company have had two months to turn a shoestring campaign existing only in the person of John McCain and a few aides to a fully-staffed general election machine that is supposed to rival the one constructed by the supremely wealthy, supremely disciplined, supremely volunteer rich Bush campaign in 2004.
(7) Fundraising has been the governing imperative of McCain's schedule for most of the spring. His campaign had to raise about $50m until the convention, and in order for them to raise that money, McCain had to travel to where fundraisers live; the political schedule has been fixed around the fundraising schedule, and not vice-versa.