I finally beat Magusar in SS. Took a few tries but I finally got him. The ending makes no sense though. I defeated him yet after the cut scene and credits but I'm still in a cage.

Did you defeat both of his forms? I'm not sure but you might need to finish all of the main story quests in order to actually beat the game. And there are two endings.

It was all a dream! :p

I'm playing a bit more Jacob Jones. Still really digging the art. It's a really charming game... perfect for relaxing on a Sunday afternoon...

Me too. And 20 trophies are a nice +.

Its a hunting game of sorts, so, going by every hunting type game such as monster hunter, gods eater burst, ragnarok odyssey and the likes, even after killing the big bad nasties, they're still there! OMG! There must be sume kinda time space warp in these games where everytime you supposedly finish the game, you end up back to just before finishing it ahahahaha!

I did finish the main quest and I was aware that there are 2 ending. I noticed that I unlocked several Avalon pact after beating him.  Maybe I have to complete those and then defeat mMagusar?

I'm not sure what you are looking for. The ending made sense, after beating the game you get to keep playing post-game. A bunch of games do that.

As for the endings.

Ending 1

Save

You decide to spare Magusar but in time he transforms again and you, in Librom's place fight him in never ending battle again. Until you decide to transform yourself into a book just as Librom did in the hopes someone else will be able to end it once and for all.

Ending 2

Sacrifice

You decide to sacrifice Magusar as Librom requested. Magusar's sacrfiiced soul meets Librom and they find peace. The Challice accepts the sacrifice of Magusar and returns the world to normal.

No, you still beat the game. It just lets you replay any of the missions with your character. It's just allowing you to play post-game. You're trying to read into it too much.

I know it allows you to replay the game but I'm just saying that because I restored the world and killed Magusar, I shouldn't still be a slave trapped in a cage in a barren, decayed world. It makes it seem like all of that led to nothing.

It resets to before your decision to fight magusar, so that you can fight him again. It all led to the ending and the credits rolling. There's nothing else after that.