Hmmm, I don't know. It seems like the Maria of past and Maria of present are two completely different players. Given that 2006 and 2012 were her best years, I'll use those terms in order to avoid stupid names like "Maria present" and "Maria future"
Consistency: In terms of results and play, 2012 Maria takes it (although 2006 Maria was very consistent in results, but not that much in actual game). Though I guess a factor was opponents then and now, but still. Maria's shots now are more reliable, she doesn't make too many errors (apart from off days) and is a more stable and patient player, hence the success on clay.
Power: 2006 Maria. I've noticed a big drop in her 'power level' after the shoulder injury, however it's understandable. While she is still powerful (one of the most powerful players on tour after Serena, Petra and maybe a few others), she hits the ball a lot softer now.
Fitness: Definitely 2012 Maria. Hogstedt helped Maria immensely in a way that she is able to endure multiple 3 setters in a row and not get fatigued. She rarely looks tired on the court, she is usually full of energy.
Movement: 2012 Maria again. You could hardly find anyone slower than Masha back in the day, but she made up for it with great power. Nowadays she can run relatively fast and while she isn't the best mover, she can defend better now thanks to her improvements. It has helped her out a lot on clay.
Serve: No competition really. Her life would have been much easier if she hadn't gotten the injury and her serve remained the same. Her serve was her weapon back in the day and imagine if she had it now! It definitely has improved from 2009 with each year and last year it was good, however 2006 was still better.
Forehand/Backhand: Arguable, but 2006 in my opinion. There was a lot more power on them and even tho she made more errors, they were harder to return and she made quite more winners as well.
Match-ups: If the Maria of 2006 was playing now, I don't think Vika would be able to challenge her as she played players like VIka all the time in 2006 and usually won easily. Also, with the 2006 serve + forehand, she would be able to challenge Serena, even beat her, I'm SURE.
Fighting spirit: 2012 wins this one. She was always a tremendous fighter, but once her serve completely deserted her in 2009 she was forced to fight for every single point(tho the serve has been very good throughout 2012 and it's getting better again). Also, after she was nearly forced to never play tennis again, I think she put things in perspective and generally became a more passionate person. It's not like she wasn't but it magnified.
Mentality: Definitely 2006. Maria is mentally strong, however she is also prone to complete meltdowns in finals, because she is Russian
If 2006 Maria was here, she sure as hell would have won the AO, IW, Miami (especially) and most likely Beijing final
Aside from Serena, I don't think anyone would be a favorite vs her in the final, whereas now, you never know
(Miami, Rome vs LI even tho she won, etc.).
Both have their weaknesses and strnegths, but I give the edge to the past Maria, even though this new, completely different Maria has been an amazing player and deffo getting back to her best. In my opinion, 2011 was also a good year, but 2012 was just epic. Basically, her only weak years since she won a Slam in 2004 were 2009 and 2010 when she was coming back from injury