What is Voldemort's real agenda?
I've seen the whole Dumbledore versus Voldemort as more of an internal power struggle within the Wizarding World and less of a real ideological one, since the whole anti-Muggleborn agenda came in well after Voldemort started his rise to power. He aspired to Dumbledore's position as King of the Wizarding World's Hill well before he was able to mount a credible challenge to Dumbledore.
It may even be something of a red herring for him -- simply a means to an end, that end being gathering more followers to his banner. He may simply have found it an expedient flag to fly, one that made it easier for him to recruit followers by using the pre-existing anti-Muggleborn bias of the purebloods and any wannabe half-blood arrivistes who aspired to join the Wizarding World's almost-exclusively-pureblood upper class.
This anti-Muggleborn bias is one that I believe may be founded in the belief that Muggleborns weren't assimilating into wizarding culture and were instead diluting its ancient traditions with their new-fangled Muggle attitudes and ideas. (Witness Hermione and S.P.E.W., for example . . . ) The anti-Muggleborn fanatics may see this issue as a struggle for the heart and soul of wizarding culture.
The analogy I'd like to draw here is the anti-Western-culture bias of certain parts of the Muslim world, where things considered normal in the West are denounced as being "un-Islamic" and serve as recruitment fodder for Islamic fundamentalists, including those with terrorist tendencies. The Death Eaters are Voldemort's own personal terror squad, bent on creating mayhem and sowing discord, but with a political agenda. Their agenda is to sap Dumbledore's public support, much as the Madrid terrorists' train bombing was a factor in Spain's elections and subsequent withdrawal from the situation in Iraq once the newly-elected Spanish government was in place.
Voldemort's real agenda may simply be to usurp Dumbledore's place as primus inter pares in the Wizarding World.
It certainly seems to be more in line with Rowling's portrayal of him as a megalomaniac. In psychiatric terms, Voldemort suffers from narcissistic personality disorder, apparently co-morbid with schizoid and/or antisocial personality disorder. (Compare his behavior, description and personal history in canon with the DSM-IV-TR diagnostic criteria for each of these personality disorders if you don't believe me.)
Some of the hallmarks of narcissistic personality disorder are a sense of entitlement and of being "special" and inherently superior. Since Voldemort is the Heir of Slytherin, he feels entitled to lead the Wizarding World.
Unfortunately for him, Albus Dumbledore is the de facto ruler of it, a situation that grates on the former Tom Riddle. This is something he cannot allow to continue and so Voldemort seeks power, by whatever means he can find, to usurp Dumbledore and become the new leader of the Wizarding World.
The fact that Muggles and Muggleborns are eliminated along the way is merely the icing on the cake, not the cake itself, since he never cared for them in the first place anyway. Voldemort seeks power for personal reasons, not ideological ones -- anti-Muggleborn ideology is simply a means to an end for him, albeit a means he exploits ruthlessly in furtherance of his personal goals. It is important to also not forget either that he had almost achieved those goals before he made his capital error of going after the Potter family, something which I am sure spurs him on to try once more to achieve his ultimate goal -- dominion over the Wizarding World, his rightful domain.