It is correct to not change the formula for one person. It's been the same for everyone else every year, too. There is no logic behind making the exception, only emotions.
there actually is logic in it, that it's a bit strange that arguably the most successful grass court player of the last 5 or so years is seeded underneath a player who has made 1 QF at Wimbledon in 10 appearances
I think there is clear cut logic in rankings as well, but in this case Wimbledon does use a format in which they consider the previous seasons results. this seems to be a rather subjective format- a logical person would wonder whatever made them make a format that counts only last season's success? if they're using past experience to explain the level of a player what scientific data says that only one previous result matters?
obviously it is the most recent or relevant, but I can see how someone might question the whole thing, when Wimbledon already has a rather unusual formula that in this case does not help at all.
they made the formula so people wouldn't be seeded too lowly based on their merits, to prevent situations like this from occurring
obviously it is what it is, but there is certainly a logical argument that Nadal could have been seeded higher just based on his incredible consistancy here
i.e. made final in 2006, 2007 won in 2008, didn't play in 2009, won in 2010, made final in 2011. since 2005 in the times that he has played he has only once lost early- 2012
this is one of those rare situations where I think they should use their brains a bit more
it's not the end of the world though
if Nadal really should have gotten better seeding in the first place then he will prove it by getting past the harder odds in a big players QF