Ziggy's look is the best look.
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I'll be the odd one out and say that I like Ep.II's character designs for the majority of the main crew the most.
I am of course no artist in any sense of the word, so I am speaking strictly subjectively here. This is just my opinion as a player.
Ep.I, IMHO, had serious problems with some faces and eyes. Specifically, a good deal of characters (most noticeably MOMO, Jr, KOS-MOS and Shion) looked too much alike;
since such and such being relatives or clones or whatever was often a plot point, characters looking same(-ish) when they have no actual reason to got confusing fast.
Ep.III too could be better in this department, in my opinion. It wasn't nearly as noticeable, but close-up shots - especially character portraits beside the text window - drew attention to proportions of characters' faces. Yes, extra materials state that it was a dliberate comeback to the character design of the first game, but goddratit, those eyes are set too damn wide!
I could understand if it was used for someone in particular or a limited subset of people to enforce the uncanny valley effect or show that people that grew up in different conditions / got purposefully modified somehow looked somewhat... off when compared to others or something. But nope, there is not a meep of anything like that anywhere I could find.
And for some unfathomable reason half of the game's cast suddenly has Shion's eye color too...
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As for details:
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Ziggy could use something different for his look, I think;
it does remind me of the older anime though, especially during his more hot-blooded moments, so maybe not. His sleeves appear to have better textures in Ep.III and his model overall looks more detailed - or at least that was the impression I got. Combat animation in Ep.III was generally the worst out of the three games, but in Ziggy's case I'm a little bit torn. On one hand, his first special attack with a f*ckhuge semi-automatic BFG is coolness incarnate;
on the other hand his normal attack animations made him appear much slower and heavier than he was before.
Yes, it is a good thing that after the dev team has shifted his gameplay stats towards 'prime defensive tank of the party' they've adjusted his animations to reflect it, but I don't think the role change was consistent with what was shown before. Remember how Ziggy was introduced? That whole sequence screamed 'tactical espionage action'. And the Cyberkick! But come the third game and he suddenly loses a noticeable chunk of his speed, agility and flexibility. Without major chassis rehauls in-between, espeically when compared to KOS-MOS.
Or maybe I am just too sad to see him stomping enemies into dust go and just try to make it sound smart.
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In Shion's case, I'd have to go with Ep.II. Truthfully, I don't like what she is wearing in any of the installments, her model in the second game has a severe case of 'mitten-hands' and I don't like the sudden shift from 'sturdily-built' towards 'pencil-thin' (admittedly, this may have something to do with her suddenly losing melee attacks against non-box opponents and thus retconning her physical condition in preparation for her later bouts of illness). Not to mention the 'I don't actually need no glasses, lol' sequence. But I like what they've done to her face and the overall color-scheme for the rest of the model she has in the second game.
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chaos is dressed in who knows what in all three games. I find the color schemes nice, but actual wardrobe gets a big 'nope' from me. Except for maybe those shades in that one bonus costume of his.
I like his iteration in Ep.II a little bit more than the one in Ep.I (and a lot more when compared to Ep.III), if only because of the proportions of his face. And his demeanor in general, but that has more to do with his actions, dialogue and body language, not his visual design.
His attack animations look nice, but stretch suspension of disbelief too much (how a dude throwing around such blatantly supernatural abilities left and right did not attract all sorts of attention is beyond me), so the overall impression was 'meh, he should've had some other theme' for me.
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MOMO's design in Ep.III wins over others, if you ask me. Not to say the previous ones didn't have some nice details to them, but the third one is a). the most practical out of them and b). does not involve any flashing and undersized garments. An automatic win, really. She still doesn't look like a combatant (and shouldn't be from the plot standpoint either), but very few JRPG characters do, so...
Although I do miss her conking armored soldiers with a collapsible baton into submission, so there is that.
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Jr is at his all-time best in Ep.II on all levels. I don't know what I could add here.
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Jin's bathrobe doesn't look like it quite belongs outside of the sequence in his own house, but I still found it easier on the eyes than his Ep.III's getup, legshots or not. The suit we first see him in beats both of them anyways. His model in the last game does show him aging faster than he really should very nicely though.
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KOS-MOS... I think I'll go with Ep.II on this one too. I don't like the concept art that's shown in the artbooks (I am a firm opponent of mechanical anything looking thin and sharp;
sci-fi machinery in my opinion should look robust and sturdy, even the ultra-light super-flexible ipod-alike ones), but I do like what they came up with when it became clear they couldn't model it properly better than others (even if did make her look like something out of TRON). The 'inner skeleton', for the lack of a better term, looks both nice and creepy, yes, but I simply happen to not like how it was drawn.
Although, perhaps, not the facial structure. I can't really decide between Ep.II and Ep.III on this one. From technical standpoint, Ep.III's has more details and pulls off the 'different look without actually changing the face in an obvious way' trick spectacularly at least twice. On the other hand, the few scenes in Ep.II they bothered with giving KOS-MOS some actual on-screen performance, it shown itself admirably too. And there is the silky smooth faceplate Ep.I starts off with that really should've had more screen time... I really can't decide on this one.
What KOS-MOS is dressed in... I don't really like any of them, even if Ep.II's is the closest to what I would've liked to see and Archetype looked appropriately unsettling (however much I personally dislike the variant of the bondage theme they went with, Aliens' visual design has shown that going for sexual subtext is a perfectly viable approach in horror).
As for the various accessories, in my book less flimsy = better, so Ep.I's arsenal in general gets my vote (sans that anime scythe). Superpowered b*tchslap and comically huge mace looked more funny than effective, but I can't say that I've liked later armblades better. Revolver/flaregun hybrid would probably be my favourite even if I prefer to pretend the cutscene with it turning into ridiculous artillery cannon never happened.
The gunpod that replaced the crazy-awesome gatling wasn't that bad per se, it even combined nicely with its bigger sibling in Asher's arsenal and I was kinda sad they didn't continue that trend with similar weapon systems adapted for different platforms in different sizes all sporting that characteristic look, but it lacked severely in punch aurally, visually and mechanically. Ep.III's spinny gun of doom looked, sounded and worked the best out of them all, but if it were up to me I would have flipped the position of the barrel blocks from (please forgive my amateurish attempt at a picture) this
. /( )\
/( ) ( )\
to this (the formatting somehow ate empty space in these when I posted, had to take awkward half-measures)
\( ) ( )/
. \( )/
simply because I think that the gun having three barrel blocks but only two streams of spent casings is not enough brass for the dakka involved and should be corrected;
inverted positioning would allow for a more visually pleasing animation of one stream going leftwards, other going rightwards and the third one going downwards.
Super-special camera designed to detect Gnosis... I like all three of them about equally, even if the second one pulls slightly ahead on account of looking 'less flimsy'. Their functionality really could've been implemented better, yes, but I have nothing to complain about the visuals.
I am more or less indifferent on the subject of 'cat ears'.