I personally liked the NCR better than Caeser but I think Mr. House wants to destroy NCR, I don't know for sure there. What should I do?

Kill House, you'll be doing the world a favor.

Mr. House does not want to destroy the NCR, in fact NCR citizens are essential to New Vegas' economy as they bring in caps. All of House's plans are made to demoralize and weaken the NCR causing its citizens to question the decisions that the government has made; but I can't go into to many details sense this is the general discussion board.

If you really want to see the differences between an Independent and Mr. House New Vegas than play the game for Mr. House up until the point you can are about to fight the final battle of the game (You will receive a large message telling you this). Save the game right before this happens. Then play the final battle for Mr. House to see his ending. After that go back to your save place Yes Man in the seat of power so to speak and play that ending.

You get to see the differences between a House and Independent play through this way and can decide for yourself; personally I think House is the best choice but, to each their own . . . .