List of Questions for community feedback:
1.What do you think are the original game's missed opportunities?
2.Out of all of the innovative features created by the community here, which would you like to see implemented?
3.What would you like to see changed or eliminated?
4.Since Plus and 1.X are taken, what should I name this patch
5.How do you feel about the Magic Guns are they worth keeping?
So much to be improved, both in WOTL and Vanilla. Honestly the reason I never got into WOTL was that it was just as broken as vanilla. I'll get more into that later, but the other reason I didn't like WOTL was the translation. As you said some people love it, some hate it, but all I remember is how horrible Delita sounded in WOTL. I did enjoy the extra side quests though, it went further into the story a bit, gave insight on characters we know almost nothing about, like reis and Beowulf(only 2 I can remember besides extra delita battle), and hell who doesn't like extra content/battles? SO anyways...
1. Moar side quests/optional battles! Plenty of room, JOT5 has over 100(?) battles between marks, side battles and story battles. Throw the extra aliste battles in, make some cool new optional battles and whatever else you can think of. I always hated the fact that only generics could do propositions and some of the propositions seemed like they would make awesome side quests too.
Another thing that would be cool but might be hard to incorporate, I forget who mentioned this though, but it would be really cool to have the treasures have an actual purpose. Whether in synth, unlocking content or having some kind of effect on the game itself(like materia could add a slight boost to MA or something along those lines). I also liked the idea of the novels.
2. I agree with jumza on this one, anything you can fit in there! Lol figure out what you want and work around that so you don't have conflicts. I haven't got far into modding anything myself, but I try to keep up with the most of the stuff on here. ARH2, synth, soldier office, and fury hack are some cool ones but there is a TON of stuff on here. Emmy does a lot of stuff to improve monsters too.
3. BALANCE. It's ok to have OP characters, some people actually like having broken orlandu(I do not). Overall that should be a choice though and otherwise balance is something that all versions of FFT lack. Certain classes just completely outweigh others, it's tough, but this can really be done later on after you have released a beta and have multiple input from your players. I mean if you look at a game like diablo, they are constantly creating new patches in order to improve balance.
I also agree with emmy on spell casting( and emmy knows much more than me so

) adjusting speed itself would also greatly improve the balance issues above too, because in any tactics game speed is everything.
I'd love to see some improvement in the random battles. Souls of Destiny(Conman's FFT mod) even has quite a few unique characters encountered randomly, which made for some interesting battles.
Get rid of clouds materia blade requirement, or make it a better weapon. I'd also like to see him not join at level 1.
Personally, I liked the magic guns. They used a different formula than the regular guns which was essentially a new weapon type in itself.
Could always add the WOTL classes, or just add some new classes. Maybe a few characters unlocked through some side quests?
I'm sure there is a ton more, and some of these might not be what your looking for, but I figure more input never hurts