The overall concept of combinging both traditional and well loved genres of comic books and classic rpg medieval themes is absoulty perfect. It's fresh and new but yet traditional feeding the audience the things we love from both without it being cliche and old. Excellent idea. Kudos to that.
Story
Like I said before the concept is really intresting. The story starts off traditonal and fun then I see it's going to get progressivly serious and more mysterious with the revealing of both characters' pasts. The idea of the hand is nice and I like how it's similar to orgnaized villians (like something out of justice leage).
The missions are good but don't get stuck in that "episodal" trap. Try to stay away from making them too pedictiable. I noticed quite a few times it was "oh save the children". I think that was done three times, right? Once with Andau the vampire, another time with the introduction to the hand on the beach, and a third time when the people at the concert were distracted (I think stealing children was mentioned but I can't remember this one clearly). So watch that out.
Some plot holes are in there or things that don't quite click right. The one that really sticks out badly is Kovak stealing money from people and then paying them off to keep quite about the crimes. Doesn't make much sence even if they thought someone else was behind the stealing. He'd have to at least pay them off enough more than the orginal value he stole or else the people would just sue to get the money that they needed. You can't bribe someone with $10 when if they sue they can get $20. Threatening them with bodliy harm would have been a better move.
I really like the direction the story is going in though. Drawing in the character's pasts in very intersting and I was excited by the ending with the two rivals. Sparrow's scene especially intresting. And the way there's a mystery behind Cade's powers and how they work. Defintly character driven but I like that much better. Also keeping the story flowing through the dungeon's is a huge plus. :D
Characters
Your main characters are definlty fleshed out well. I can tell you've put some thought into them and they're dialouge is beautiful. Each character clearly has their own voice and opinion.
Cade is a do-gooder type but he isn't typical. He's not perfect like most super heros are done and I like that. The change that's been in him is instersting to see and I like how the othere characters are noticing it. I have a feeling there is MUCH more to him that he's letting on. He seems like a normal average guy but there's gotta be something buried in there. He'll be the more plot driver. Very well done.
Bones... B-man! Love him. :D He's outspoken, blunt, and super-hero witty/rude. heehee. He'll probably be a favorite for a lot of people because he's both comedy relief and serious. The way he's kind of lonely and the dealings with Rana are intresting and sad at the same time. I really feel for him beacuse of all the prejudce around him...even though it's something like being an undead it's still done in a way I think we can all relate to.
The other characters are done very well, too. I like the way you gave almost all of them catch phrases like Bones's "I know all" and nicknames with Finely calling Bones "B-man". It's very life-like and I'd have to say this is really the best dialuge by far that I've seen in an RMXP game.
My only gripes in this department would be your NPC towns folk suck. They do the job, but the'yre just mindless characters wondering around saying only one phrase. Mix it up a bit or else no one will bother talking with them and I've found myself skipping over it. Don't forget to think about rewarding the player with simple potions or something for talking with them or some other items. I mean they all live in the same town, they'll do eachother favors.
Visual/Graphics
The rtp works fine for a light game like this even though I see its going to get more serious. Consitancy would be much better though. Picking an art style with the face graphics and battlers would help blend the game better. But I see you are probably in the midst of getting that done... not to push Enkur too much, ne? His battlers for the second arc turned out very nicely... Although Auburn's battler doesn't really match with her sprite exactly. Might want to change the sprite up... the back of her looks really strange. Is that supposed to be a cape? An idea that might be intresting is I noticed Enkur's art is sorta DBZ style but what might be intresting is for style to lean more towards tradtional comic book. I have yet to see that in a game.
I think it was already pointed out but your mapping is just plain okay. There's too much open space and the buildings change shape when going in and out. Like if you go in and out of the Port's buildings they be bigger inside or change shape... If you got something 10x10 make it 10x10 inside. It flows a bit more nicely that way and makes more sence. Tighten and compact... you can still do puzzles that are visualy pleasing in the dungeon. Maybe advice from your team's artist might help or asking for a mapper...?
Music
Your choice so far has been very good. Though the problem with it is they don't really repeat correctly wich disrupts the feeling of the game a bit. There's a way with some editing programs you could do to stream them together a bit more. I mean it's harder on songs like with the stage fight but some of the other ones could be looped with a bit of work. That little extra makes a difference to emerce you in more.
BTW there's an error in Arc 2 relating to this. If you go into a certain room towards the top of the Church it will shut down because "andau's theme" wasn't included. Not a big deal, but thought you should know since it shut down on me and I had to back track.
Game Play
I like how you make your battles dynamic. From the rock men transforming to the Kobold's calling for healing members. Though in this department you could use a much larger variety of monsters. There was only two differnt kinds in each section... try going for five instead... that mixes it up a little better.
The puzzles I found were difficult but not so terrible that I was screaming. I got annoyed with quite a few of them... and most times I had to figure out the number combinations the hard way by writing all possible combinations down and then imputing each one. Could you tell me the reasoning behind neck tattoo one? I understood how to come up with the fourth neck one but didn't understand how it went with the switch.
Kovac's mansion was done well but some of the phsysical stuff like moving the vase and Bone's breaking down the door was hard because my computer is on the slow side. It wasn't registering the button input correctly so I had to go crazy and put the game on high priorty in the task manager. Though I'm most certain there are people with slower computers than mine... might want to make it a bit easier or after so many tires make it easier. Something like that isn't puzzle/thinking related and can equal hair pulling out really fast, so keep that in mind.
I found the rest of the puzzles rather enjoyable and where very well done. Just don't forget to give a little better hints. Maybe have a person try out your puzzles and see how fast they get them and perhaps making up a strategy guide since they aren't dopy-easy like some other games are...
BTW the last dunegon with the revisit to that for was very funny. I liked the comments in that one. They said exactly what was on my mind. :D