About the ultimate beast: I don't think it is cool to just have someone say "Go kill the evil beast, maybe I can make something out of it.". Here is what I think would make this sidequest much more interesting(battle and story wise):
Well, in the Zeal ruins, it is said to have absorbed power, and maybe this absorbation also made this predator a sentinent being. A sentient being as uber boss is always cooler, anyways. During it's time in the ruins, it also learned about the past of Zeal, the guru's, maybe there even were some secret scripts of them and all that stuff.
The guru's order you to find and eliminate that evil being, yet they don't tell you what their real intention is(that it might be dangerous for their plan or something). The player/party trusts the guru's and their judgement and won't question it( maybe use that against the player).
Now, a "find and kill" mercenaries sidequest might be fun, but nothing memorable, so I would say add some stuff there:
The whereabout of this "Being" is unknown, yet it is known that it lived during the Dark Ages. When the party reaches that era, they can gather info from the people living there(maybe make this being like a legend). They find it somewhere hiding(or, this being knowing about Schala and Janus by reading the Scrools it found in the ruins, could also be at Schala's grave and await the party, just for the coolness). The party should have the option to fight it or not! But before that decision, lemme tell ya what I think this "Being" should talk about(that's why it shoudd be sentient, IMO):
What I actually want to let it talk about is anti-guru stuff, that hasn't been in any game as far as I recall. It should know the guru's, and hate them, for the reason...like...it is their fault that it's species died or something...This being should question the way the party acts, as a mere tool of the Guru's, so the party notices the other side of the coins, maybe make the player question what they did. I think we shouldn't just let the guru's be the "allknowing good guys" and even if it is "only" in a sidequest where the player is faced with this stuff.
(I kinda got the idea from Gothic 3, with the exception that the partydoesn't kill the gurus heh.)
Well, after that talkie stuff, you can either fight it(where it won't be using his uber strengh to own ya, because it wants you to question what you are doing, and you can hardly do this if you are dead):
-> if you fight it, and you win: it owns you Gade's style(Lufia 2), yet still lets you survive, and then dissapears(maybe jumping into the ocean if the battle is settles at north cape, because this being is supposed to be able to life underwater if I got the text from Z right)
-> You fight it, and lose, and it just dissappears(s.a.)
-> You don't fight it, it dissapears. Yet it gives you an item that is different to the one that you can win/steal, a very rare one, and stuff.
Now, this might be the intro for the Sidequest. You go back and talk to the guru's, that try to conveince you that you have to kill it and it is evil and stuff.
You now know what you gotta do: find that thing! To kill it or to get more answers.
I thought about challenges, so to add another yet different idea(if it is possible): How about defeating copies of the party?
In order to get to that being again, you have to fight copies it made(Maybe in the ruins where it had been hiding there was some kind of cloning machine, and it got your DNA after the first fight.)
There is like a Crono & Marle, Lucca & Robo and an Ayla, Glenn and Magus copy team. Every team is somewhere hidden in an era(whereever we want to have them, one team could be the team champion of the colliseum, that you can challenger after you beat it and after you started that sidequest). The fight will be fun with letting them use double techs etc.. For each beaten team(they are uber hard and stuff, for being and uber challenge, you know) you get a hint and a key where the being is now. If you got all 3 hints, you can find it like in the Ocean's Palace(you need to know the hints to let belthasar know that he should take you there). The keys can be like the clones, you enter them into the tubes(just for the sake of seeing clones in tubes again, like in the Black Omen) in the last area to open a door where the "Being" is. This time, it realises that you are stupid and stuff and that you won't get that you are used, and that you were sent to kill it, and that it might be better to finish you off so they don't have you as a tool anymore. Like...indirect revenge on the gurus...or something...
Battles would be:
1.) (optional)"Being", a weaker form, maybe to judge your skill;
2.) The party copys: Crono&Marle, Lucca & Robo, and maybe even Ayla, Frog & Magus(it is the challenge sidequest nevertheless)
3.) Battle with the "Being", this time seriously.
Just an idea to make the ultimate battle more a sidequest and not only one battle. I don't even know if the clones are possible... it is just a small pack of thoughts, of course it isn't perfect and stuff, I just want the uber battle to be an important one(like...Dario in CC?). More or less.
And I used "stuff" and "like" just for the reason that I am not allowed to write that way in an english test.