Since this is one of the most professional reviews I've ever seen, I've decided to open this as a topic, to be able to answer/discuss it. (I hope this does not conflict with the rules).
First of all I want to thank eskimo44 for the detailed review, which is always welcome. Ironically I agree with every part.
If I would be designing the same hack (that I worked on back then) today, I would definitely change things. The main issue we need to take into consideration is the fact, that Z3 has poor editing programs, and that this hack was very bugged in beta stage. It was thus impossible to insert a title screen or expand the dark world etc.
Since Z3 dungeons are very difficult to design; maps, compasses or floor counters are really a side thing, usually bugged or impossible to do/change (don't be surprised if future hacks have those things removed completely). So when I've first seen those dungeons made by Dudeman and Omega (no puzzles were in yet!), I decided to bring them from beta state, since I knew, we are looking at the best custom/fanmade Z3 dungeons (IMO) at the time (considering the bug nature of editors, the lack of Z3 hacks, and the fact, that the creators are not a company and have limited testing abilities= beta testing is a pain, and are few in numbers). But they are still not a match for Alttp dungeons.
Regarding the bosses. Not really much you can do with the programing. Brand new bosses are a far dream in Z3 and would require "impossible" asm, so Z3 has always looked into gfx changes of bosses. The new upcoming Parallel Universes hack by SePH is really doing an awesome job on this.
Regarding the overworld. Altogether unfinished in my opinion. I did add a lot of new areas, but essentially decided not to use the entire capabilities of the overworld. Partially due to bugs, partially due to a poor editor capabilities of 64x64 map drawing system. The game also had a strange crash bug when jumping diagonally-down from all cliffs (the result are some unaesthetic fences).
Sidequests and story were a side thing. I didn't spend much time with that, since I thought players like to play (not read) the game. I don't like reading when playing and a lot of players don't understand a word in English. But it seems many players actually favour the reading part (something to look into in the future). The same with sidequests/ sidegames.
Regarding the gfx. I was a gfx rookie back then. Considering what I can do now, the gfx part has minor changes in the hack.
Regarding the difficulty. I would make it easier today, or at least also make an easier version, since a lot of players find it to difficult. Since armor2,3 and shield3, sword4 were considered to powerfull, they were removed. Today I would insert them back (at least armor2).
Regarding the standout criticism. That Master-sword-pit-room would go out today, but back then I thought of it as a challenge. The same with statue puzzles and "super" ice-thing-throwing puzzles. From experience I've learned to either remove statue puzzles or make them a lot smaller (quarter room only). The same with special puzzles and challenge rooms.
Of course the current Goddess of Wisdom will not change (new painfull beta testing would be needed; unstable, bugged if edited and generally "unclean" current rom; multiple versions already to this date, which confuse players; working on other projects etc). But we will look into all what has been said with our future projects.