Not particularly. If we wish to talk about motives for a second, the motive of wishing to compare Dhoni to Pietersen will likely be simply to raise that India's best ODI batsman is superiors to England's.
Out of sociology and on to the thread topic at hand. Earlier, I took the cop out approach but I'll look to simplify for the thread topic and look at who is the more effective batsman.
Starting point is to eliminate averages from runs scored against any non country (World XI, Africa XI, etc), any non Test playing nation, Bangladesh and Zimbabwe. These runs will be seen as moot from here on in my analysis.
Dhoni: 45.82
Pietersen: 48.29
However, the situation becomes one of current form as Dhoni's recent form has been superb and Pietersen's merely very good. In 2008, Dhoni had 988 runs at 52.00 (as well as three fifties in 2009 in five innings) whereas Pietersen had 658 runs at 43.86. However, this is not sufficient justification to say that Dhoni is a better batsman, merely that he is in better form. Dhoni has shown weakness in Africa, Europe and West Indies whereas Pietersen has solid form in each continent except Oceania, which is still adequate (265 runs at 33.12). Pietersen is clearly the more rounded batsman for dealing with difficult conditions, the best test of a batsman. Moreover, Dhoni's recent form in 2008 and 2009 has come mostly in Asian conditions. Not exclusively flat pitches, but subcontinental pitches nonetheless. Now, Dhoni has succeeded in Australia and he may have really turned the corner in the past year with the captaincy, but it has not been fully proven as of yet.
The point about match winning ability is an extremely intriguing one. Pietersen has seven ODI centuries whereas Dhoni has just two against top quality sides. In wins, Pietersen averages 83.33 (strike rate of 93.28) compared to Dhoni's 70.32 (strike rate 99.04). However, Dhoni has played in 54 wins compared to Pietersen's 21, a far superior percentage of 52% (wins/innings x 100) compared to Pietersen's 30%. Many other factors play into this particular statistic, but still interesting.
Dhoni is one of the all time great finishers, and tremendously versatile in moving through the order, but for the simplication needed to provide an outright winner, this must be ignored for obvious reasons (Pietersen is not a finisher, only bats in one or two spots, etc). But my call is that Pietersen has proven himself the more effective run scorer. Pietersen scores all over the world and is only hindered slightly by conditions whereas it is much moreso for Dhoni. Dhoni is in better form, but I have shown that not too relevant. Dhoni has played many more ODIs which helps his credentials somewhat but not entirely.
