But since you are directing the dialogue doesn't that mean you know which lines you will need and when? Can't you rely on breaking them up in easily manageable bits based on location, character or storyline?
Is there a downside to setting the limit at 10000 or higher? I have little idea if that will be enough. Estimating the amount of dialogue lines for a game genre is impossible if you ask me. RPGs in general could easily be very limited if done as solo project but they could just as well be massive for big teams where submitting dialogue and scenes is made easy.
Some games have their dialogue line amounts published (mainly for evaluating the amount of voice acting work) as I just did google search for "lines of dialogue in x".
Mass Effect 2: 25 000
Skyrim: 60 000
Fallout 3: 40 000
GTA IV: 80 000
Dragon Age: 68 000
EDIT: I am aware these are not JRPGs but it seems to be hard to get info on them
Is there a website you are getting this information from?!? This would be very useful to my cause