In the classic story Genesis of the Daleks, the Time Lords send the Fourth Doctor back in time to Skaro's past to alter Dalek history, and at the end the Doctor says he's succeeded in setting their development back by a thousand years. So how does this affect all the Dalek stories that happened previously? The Seventh Doctor mentions the Dalek invasion of 22nd century Earth as though it's still valid in Remembrance of the Daleks. And I know they aren't strictly speaking canon, but the Eighth Doctor comic strip story Children of the Revolution refers to the events of Evil of the Daleks, and the Tenth Doctor novel Prisoner of the Daleks seems to me to take place round the time of the Dalek conflict in Frontier in Space/Planet of the Daleks (although for some strange, unexplained reason, the Daleks here more resemble those of the Time War era, which is a bit odd).
And then there's the fact that in their early stories, the Daleks used static electricity, but in Genesis they seem to have their own power source, which I don't think has ever been addressed.
And then there's the fact that in their early stories, the Daleks used static electricity, but in Genesis they seem to have their own power source, which I don't think has ever been addressed.