Yahoo!'s (NASDAQ: YHOO) preliminary proxy came out this week and it was all over the news that CEO Marissa Mayer's pay had gone down -- to $26.9 million in compensation in 2013 from $36.6 million in 2012. Quite the drop. Especially as she only worked six months in 2012.

The real truth, of course, is not reflected in these headline figures. Mayer's take-home pay in 2013 was over 300% higher than what she earned in 2012, and not just because she was appointed part way through the year and only received half her $1 million salary. The big rise is because around 760,000 of the restricted stock units (RSUs) she was awarded as compensation for loss of earnings at her previous employer and other elements of her sign-on bonus vested during the year, with a value of more than $20 million. Thus her take-home pay in 2013 was $24 million, compared to $5.9 million in 2012.

Those RSUs were part of the total $35 million sign-on bonus given in 2012, when they were allotted an estimated value much lower than what they were eventually worth in 2013. That growth in value was because the company's stock price has gone up so much under her leadership, from around $15 when she joined to almost $36 today.

Is Mayer worth it?

Mayer personally owns over 650,000 shares of Yahoo! stock, and there is still a lot of stock from the original sign-on bonus sitting out there waiting to vest, so she is pretty exposed to the company's stock price and presumably concerned about its value. Of course, the equity award that vested last year was restricted stock units rather than restricted stock, and it's likely they were paid out in cash and therefore not exposed to the stock price downturn that occurred in the last couple of months of 2013. But she still has plenty of skin in the game.

Interestingly there are no shareholder resolutions calling for pay reforms on the proxy, despite the massive waste of shareholder cash on hiring and firing COO Henrique de Castro. However, this year's Say on Pay vote will be interesting.

So is Mayer worth it? So far, it would seem so, but it's early days. Her spending spree on mobile apps and, probably, the Alibaba effect meant that Yahoo! actually made money last year -- something it has struggled to do for many years. Advertising revenue is up slightly and there are rumors that Yahoo! is attempting to dislodge Google (NASDAQ: GOOG) from Apple (NASDAQ: AAPL) products, which would be a coup.

However, there is something of a disconnect between pay and performance at the moment. Mayer has already earned a great deal of money from the company although the returns to shareholders have thus far been minimal. Future compensation depends only partly on future performance, much simply vests over time.

But this is how the package was designed, with large amounts of up-front payments to induce her to take the job. That it was designed in this way, however, does not make it right. Too little of the total package is fully performance-related, too little is truly long-term. And while it may have been effective at getting her to take the job, there is no guarantee of its effectiveness from a shareholder point of view since much of the pay will be delivered regardless of performance.