This isn't anything like the end of the series (Star Wars or NJO) - what they're doing (personal speculation, not spoiler) is putting the New Republic back in a situation where it's best suited to be - a Rebellion. Once again, it's a bunch of little guys fighting the big guys. The New Republic was getting too big, overgrown, beaurocratic, etc... - they had to make things smaller again, hence they *SPOILER* gave Coruscant to the Yuuzhan Vong. *END SPOILER*
Oh, and from what I've read, *SORTA SPOILER-LIKE THING*Anakin isn't dead. *END SPOILER-LIKE THING*
Now whether the execution of the above sorta spoiler-like thing is done tastefully or stupidly is a matter that will soon be determined.
--TurboNed