They're his nemesis, his archenemy, and honestly, he's so tired of fighting them. Every time he thinks he's done it, finally defeated them for good, they show up again like the proverbial bad penny.
Why won’t they just die?
The universe doesn’t need genocidal pepper pots, everyone would be better off without them, but it’s almost as if they’re genetically encoded into the very fabric of the universe so that no matter how hard he tries, he can never completely eradicate them. It makes him feel like tearing his hair out in frustration, except that he tried that once and it really hurt, so he’d rather not do it again
One day, it would be so nice to be able to say, “Oh look, no more Daleks, isn’t that fantastic?” And it would be, he feels sure the entire universe would celebrate with him. But it’s never going to happen.
Perhaps it’s a matter of balance; for him to exist, they have to as well, to give each other a worthy opponent to do battle with. If anyone had ever asked him, he would have said he really didn’t mind battling un-worthy opponents, or not battling anyone at all. Actually, he’d rather like that; never did like fighting really, he doesn’t hold with violence. Everyone getting along peacefully would be so much better. Of course, no one ever asked.
So here he is, and here the Daleks are, and once again he’s got to fight them.
“Haven’t you had enough? You have to know by now that you’re not going to win. Why won’t you just give up and die already?!!!”
Might as well be talking to himself really.
“See? I knew you were going to say that! You’re so predictable! Ah well, here we go again, and may the best man win. Or the best Time Lord as the case may be. GERONIMO!”