As you alluded to, the original run of Doctor Who had the Daleks "wiped out" repeatedly as well. Since you only list the 2005 and onward, though, I will stick to that. I'll first clarify your points:
* The Parting of the Ways, <PERSON> destroyed all the offending Daleks in the fleet created from the DNA of <PERSON>, along with the Emperor himself. At that juncture, no one involved in that story knew other Daleks survived. Even assuming <PERSON> had knowledge of the entire universe (which, there is nothing to indicate she did), they were outside the universe in the Void at this time.
* Doomsday involved Daleks who had hid out in the Void at the end of the Time War, avoiding demise in all previous episodes. There were two groups - those from the <PERSON> prison, and the Cult of Skaro. The Cult of Skaro used an emergency temporal shift, and the rest were sucked into the Void. In The Next Doctor, it is revealed that these Daleks in the Void were working on a way out, which the Cybermen stole. These Daleks may yet return.
* Daleks in Manhattan/Evolution of the Daleks - <PERSON> survived, as you point out.
* Journey's End - These Daleks are not the original Daleks, they are new creations from <PERSON>' own cells, but like the previous Daleks, they go against him. The Metacrisis Doctor is the one who does the destroying, not <PERSON>, by sending what amounted to a self-destruct signal. 837
There are many excuses possible, but none specified as to why a few Daleks did not self destruct.
* Victory of the Daleks - It's World War II. <PERSON> makes reference to World War I, but it is shown in the episode that he isn't really that old.
To your first question, "aren't the Daleks cheating against the Doctor?" - All is fair in love and war. This is at least war, but Asylum of the Daleks implied the other might apply too. The one item you reference that is "cheating" is <PERSON> breaking through the Time Lock - and it is stated in the episode what happens here. <PERSON> lost his mind in the process, being exposed to the vast temporal energies of the paradox his involvement was creating. This insanity is precisely why the Doctor doesn't break the Time Lock - that, and it's explicitly stated in The End of Time that the Doctor was intentionally responsible for <PERSON> being caught in the Time Lock due to the horrific plan <PERSON> had to win the war. In short, the Doctor felt that the Time Lords were a greater threat to the universe than the Daleks.
To your second question, "Why doesn't the Doctor go back to a time before the Time War (which is not time locked) and "breed", just like the Daleks?" - He wouldn't need to time travel to produce more of his kind, if that were his goal - the children could just travel after they are old enough. I think you are actually asking why he doesn't go back to Gallifrey and do something about his people. The reason for this is that the Time Lock encompasses the Time War. They have shown in The Invasion of Time in 1978 that if you are in a war as a time-active people, the first thing you try is to time-loop the enemy's entire history, which means all of Gallifrey's relevant history is locked. He could potentially have children, and inadvertently did with <PERSON> (who was shown to still be alive) in The Doctor's Daughter, but given that he intentionally destroyed the Time Lords, he wouldn't be recreating them unless there was a new plot-driven motive. 837