Because Keynote changed so much it doesn't automatically overwrite the old one as some people may want to keep on using the old one. (That was certainly the case with Numbers where they took away so much functionality with the new one that I only use the old version.)
If you follow the instructions I gave above it will change your Mac so that it only uses the new version of Keynote for all Keynote files on your Mac.
Then when the new version of Keynote is running (It has the blue icon, not the brown one), you can right click on the dock icon and select Options -> Keep in Dock to keep it in your dock. Likewise, you can select Options -> Remove from Dock to remove the old version (brown icon) from your dock.