I found him amusing in SB but he's a one-trick pony to me. Once you've seen him in action a few times, it gets dull pretty quickly. One thing they're compensating for a bit with Fandaniel is how apparent failure in realising his plans doesn't phase him overly much (this is something they did with Elidibus as well, of course), which creates a sense of intrigue as to what he's really trying to accomplish through his schemes. The fact that he wants to die but in a way that erases all existence (which would probably require the destruction of the Aetherial Sea too) means it wouldn't suffice for someone to simply "kill" him, as he could achieve that right now and simply not use his dark crystal. He wants something much more thoroughgoing.
Unfortunately, none of the "themes" that supposedly exist in Zenos do much to interest me and I don't consider him to pull them off particularly well, to the degree that they're even themes I care about.
There's hints of this in certain interviews they did re-jig aspects of the story, so I'm inclined to agree with this. Elements of the story they went with (e.g. Elidibus's Primal nature, as well as the memory loss) just about barely worked if you don't look too closely.
Regarding Ishikawa, I believe she's competent enough, but in the end, character popularity seems to play a big part in their decision making, and it can fluctuate quite a lot, and is a likely constraint that can force last minute changes. In particular, I suspect they may have had more planned for Elidibus, but Emet-Selch took a lot of his thunder, and his rather meteoric popularity must have been too tempting to resist putting to use, plus I am sure they began to grow leery of the fan reaction of terminating the Exarch for good. IMO 5.3 was a mix of good (ancients'/Elidibus backstory) and bad (much of the rest, afaic), and I was disappointed in some ways, because I was expecting great things out of Elidibus following 5.2... not for him to be dispatched summarily by 5.3, a mere few patches after Emet was taken out. Elidibus and Varis were two of my favourite characters.