Perhaps we could provide little hints to the player by letting characters talk to each other. As time passes, the characters would give larger and larger hints. Thus, the player will be encouraged to figure it out themselves (since they have to wait otherwise), but if they can't, they get hints automatically.

(Syne talks to Enna)
Syne: What do you think we should do?
Enna: I wouldn't mind putting a few arrows through those Pylos scum.
Syne: Enna... these are real people. They don't know what we do. I was one of them once. I'd like to avoid hurting them if we can, although I can't think of any way to do that right now.

(later)
Syne: Still thirsty for blood?
Enna: Oh yes.
Syne: Thought of anything?
Enna: Nothing you'll like.
Syne: Tell me anyway.
Enna: Well, they only have spears... If I could find my way to the top of this cliff... But that still involves violence.
Syne: I'll think about it.

(later -- automatic)
Enna: Hey, Syne!
Syne: Yeah?
Enna: See that loose rock up there? Right over the cliff? I bet Cade could push it.
Syne: (looks) ... You're evil.
Enna: Who isn't?
Syne: Point.

(Talking to Dell)
Syne: Whaddya think?
Dell: I don't wanna fight. Those guys look mean!
Syne: Yeah, well, you got a better plan?
Dell: ...

(later)
Syne: Got anything for me?
Dell: I can fly.
Syne: (sarcastic) You don't say. But how will that help?
Dell: I don't know, man. I mean... no... no, I don't know.
Syne: Hmmm?
Dell: Well... the only thing I can think is to distract them somehow... they wouldn't be able to hit me if I were 20 feet up! But I still don't wanna fight.
Syne: That might work.

(later -- automatic)
Dell: Yo, Syne!
Syne: Hmm?
Dell: Do you see what I see?
Syne: Apparently not.
Dell: Some dude on the fourth floor left his window open. Look!
Syne: But is anyone inside?
Dell: I can't tell from here.
Syne: Well go check it out, then!
Dell: Aye aye, cap'n!

(Talking to Cade)
Syne: Any ideas?
Cade: Pff. We could take them.
Syne: I dunno. They look tough.
Cade: Yeah, well, so am I. Besides, they're probably not too smart.
Syne: What if they call for help?
Cade: Well, we'll just have to kill them before that, won't we?
Syne: (grumble)

(later)
Syne: Got any better ideas?
Cade: Well, if you're really so scared of them, we could make the situation a little more favorable.
Syne: What do you mean?
Cade: Set a trap. Get them when they aren't expecting it.
Syne: Wouldn't that violate one of your codes of honor or whatever?
Cade: Tactics! Being honorable doesn't mean being stupid! Surprise is a significant advantage, and only a fool would pass it up.
Syne: Uh-huh.

(later -- automatic)
Cade: Hey! Wait a moment!
Syne: Wha?
Cade: Do you still have your Pylos uniform?
Syne: Yeah, I... uhh... gee, you'd think we would have thought of that sooner.
Cade: Heh heh.
Syne: But they'll be wanting ID, and somehow I doubt we're cleared to enter.
Cade: Hey, these guys are dumb, remember? We'll just play with their heads a bit.
Syne: Real honorable.
Cade: Silence!

Won't doing that for all/most battles be a bit complicated/annoying?
Also it would require highly interactive environement... like being able to push boulders or have trees burn to get the guards' attention. Once again 2D would make that A LOT easier.

In addition to all of that, in really increases replay value. It sucks playing an awesome RPG only to beat it and not be able to go back through and find anything new, because either the storyline has been fulfilled or the choices that you make have no impact.

Now, here's what I'd like to know... is this game going to be played in 3rd person, with control over all characters/being able to assign all of them, or will it be that the person is in control of Syne and the rest are run by AI?

I say that Syne not be a 'main' character in the sense that he is not equal to the other character in terms of control. In Kingdom Hearts, for example, you played only Sora; in this, I say you should be able to switch 1st-person control between all of the characters. i.e. switching from Sora to Donald to Goofy, etc.

Well, right... the puzzles should always be solvable without hints.

In the situation with the puzzles, I like. And then to be able to have the other characters give hints if you ask them about something, although I think the game should give the player a couple of selections. That would make the puzzle easier to solve. For example, when asking one of the other players what to do, there could be a couple of suggestions. Like asking if the character can fly into an open window or asking if the character can distract the guards.
I just think that choices add to the gameplay a little more and add that bit of being able to control the game as a player more.