The Conquest Blu-Ray has both the PG-rated theatrical cut, and an "unrated" extended cut, which has the alternate ending, much more blood and violence during the "uprising" scenes, and the proper score during said scenes (as, when they had to cut the violence, they had to scrap the score and track the main theme throughout the battle).
The ending is better, mainly because it leads into the original Planet of the Apes better and makes Battle redundant and unnecessary (which is good, because Battle is a terrible movie).
In case you're curious about the specific differences: