to begin, let me say that overall, I really liked the addition of the Pandora's Box and Shadrack puzzles, I do believe. They added a pleasant variety to the gameplay mechanics. I do, however, feel that they might have been more effectively introduced a little earlier in the episode by smaller, easier versions of themselves, training players in these new gameplay elements. Indeed, it may even have reduced the aversion that some feel to them, being perhaps more likely to have been seen as more complex versions of pre-existing elements rather than new elements suddenly included.
The Pandora's Box:First of all, I really like the overall puzzle mechanism, and I agree with keeping that section being implemented in gameplay rather than a cutscene. I very much enjoyed the artwork in it, by the way: a lovely, mystical atmosphere, joined with urgency and threat from Shadrack.
As to the mechanism itself, my only real complaints were the place-swapping, the narrator being still active and, to a lesser extent, the top icon-bar being still active, which all added some degree of frustration. The first was slightly mitigated by my learning, in time, to identify the circles by some reasonably distinct element, but even so the movement and fading of the circles meant that I didn't always identify them before they vanished again. The narrator, combined with fading or moving circles, became a little annoying, as I recall, and at that point superfluous, I feel. the menu-bar issue is a niggle: at times I wanted to select an element that happened to be near the top at that time, and found the bar getting in my way.
The Fight:I enjoy the concept here: it could well have been a rather fun sequence for me, I believe, and again I feel that the artwork was good, if perhaps less impressive than that of the Pandora's Box scene. The attack animations, by the way, were both pleasantly varied and at times amusing (clearly Shadrack is not quite a "squishy wizard", given what he stood up to.

).
My main disappointment here was that the Earth attack was the only one that worked throughout most of the fight. This is perhaps not in and of itself a flaw: the main puzzle is reacting to Shadrack's actions, not the counter, I feel. However, the sequence was presented suggesting that Fire was likely to be useful, if only I looked for the opening, leaving me feeling that an attack was wasted. A solution might have been to either provide a Fire attack that has use in the main combat, or to not allow access to Fire until it becomes useful.
Shadrack's lightning attack has been mentioned a few times, I think: I don't think that I ever figured out where I was supposed to look for that. Instead, I was watching Shadrack, and thus missed the cue. Perhaps a slight pan up might have cued players to look to the sky?
As to the smoke attack, I seem to recall being a little confused about that one, as I don't think that it ever seemed to touch me; indeed, I think that I at first took it for a teleportation on Shadrack's part.
Finally, as to Shardack's "rocking the boat": I think that the only problem here was initially not realising that the arrows on the amulet were dodge buttons. Again, I think that this may be a player-training issue: previously - just prior, perhaps most saliently - dodging has been achieved via clicking to one side or the other of the character, accompanied by white text, meaning that that was likely the expected interface (and I do seem to recall that I looked for just that). For preference, I think that I would like to keep the standard mechanism, since that is what the player is trained in. If, however, the new mechanism is to be included, then perhaps highlighting the arrows a little more might be helpful: making the arrowheads larger, and perhaps flash briefly the first time, for example.
Implementing "adventure" and "action" options:More work for you, I daresay, but it could work, I do believe - although note that I don't think that it entirely fixes some of the points that bothered me, at least.
Thoughts:The duel with Mordack has been mentioned, I believe. One idea for an alternate approach to such sequences that might be more interesting than the duel in this episode might be to give the player a set of actions that they can take, each with some effect. The enemy then has another (perhaps overlapping) set of actions, again each with some effect. These are then chosen by each in more or less the same system that you have, albiet with more time to think, given the greater number of options: one side acts, the other reacts, and then places reverse. Notably, the effects of one action may cause the one affected to become more vulnerable to another, and the logic should be set up such that repeating a small set of actions over and over fails. The challenge is then to manoeuvre and manipulate your opponent, while avoiding having the same done to oneself and taking advantage of said manipulations and manoeuvrings.
For example, the player might find themselves in a spell-battle; they have access to an ice spell, an earth spell, a fire spell and a wind spell, as does their opponent. Said opponent is standing on a short pillar, not tall, but tall enough to keep him away from the flames of their fire spell. Their opponent might himself cast a wall of fire at the player; the player counters by casting ice on themselves, creating a zone of cold that negates the heat of the fire. If, however, they had used wind no effect may have been had on the flames, but the opponent might have been knocked from the pillar, leaving him vulnerable to the player's fire on a later turn.
The above is probably far from the best that might be done with such a system; indeed, I suspect that, with some thought, a confrontation might be made that plays as combat but which is effectively a boardgame in logic (without necessarily including anything like an actual board or set positions; states may take the places of the board).
... but it's a shame that adventure has never been allowed to evolve ...
Personally, I would love to see more new mechanics appearing in adventure games, I think, and to have games of both the old styles and new styles, and likely too hybrids of such.
For that matter, as someone who is very fond of the Quest for Glory series, I think that I'd also like to see more Adventure-RPG hybrids, which I feel worked rather well in those games, and could likely be improved upon.