I misremembered or misheard the lore that the 12th Doctor is evil. The kernel of that lore is actually "Trial of a Time Lord" wherein a character called The Valeyard is described by The Master as The Doctor himself, but a distilled version of himself from between the 12th and 13th regenerations. So, that's kind of a different thing.
I still find it fascinating to watch The Doctor struggle with madness and the possibility of evil. The lines he tosses out are just such typical Evil Genius fare. Like, "Is nobody going to thank me?" Expecting shocked and terrified people to be grateful. And of course the biggie. "The laws of time are mine, and they will obey me." Ice water down the veins, I'm telling you.
This episode was truly visually captivating as well. In honor of which, I've put a bunch of screencaps at http://springdew.com/images/livejournal/WatersOfMars/ - they're all jumbledy and out of order and oddly named, but these are the moments I love best. Look at Tennant's incredibly expressive face as it expresses helpless bewilderment, realization, determination, rage, etc. and so forth. Love these.