The VN part of Honey is, as you would expect, dialog heavy, and it's been quite a pain to set up. Even for simple dialog, if you wish for anything more complex than a simple message background+line of text that doesn't go beyond that single message, it requires a lot of variable and organizational work, as you said. Best advice I can give is to setup a whole event page dedicated just to that, and you call that page whenever you need dialog around - and then, you comment like crazy to find your way around each individual dialog event!
For Honey, just for the mechanical workings of the VN segment, no plot event and the likes, I have to use about 700 different events (I'm speaking dialog events only here - for the function calls that make everything work, there are only 5 or so). Of course, that's for a VN which heavily rely on multiple choices, so for a JRPG, if you're only looking for "normal" dialog with minimal player input, you should be able to manage with a lot less, with the caveat that unless you variable like mad, each individual message would be a different event, or close to it. Of course, that's using my system - if anybody's got anything better using C2's visual script, I'll be interested too - though it's already far too deep in the rabbit hole to change for Honey at this point - but for next time :-D
EDIT: I should clarify that my take on things only apply if you intend to use C2's visual scripting. If you can do external scripting or use other languages, as shown below, there are far better and more efficient ways to get a dialog system done :-D
And just to show something new, since I'm not posting much these days because it's only animation, animation and more animation :