Disappointing, but honestly unsurprising.
VLR's existence was the result of 999 becoming an unexpected sleeper hit in America. Hitting that kind of success twice is
much easier said than done. The Phoenix Wright games, for instance, have sold less and less with each entry even though the first was a relative hit.
I wouldn't be surprised if a big part of the pitch for VLR was "we'll have strong sales in America,
and we'll change it to get better sales in Japan." Uchikoshi's confirmed that VLR has less gore than 999, for instance, because they expected that to sell better in Japan. They also made a short animated PV and some pretty fanservicey side stuff in the leadup to VLR's Japanese release.
And then VLR, well...
This is from Road's website, it uses Famitsu numbers.
NDS Zero Escape: Nine Hours, Nine Persons, Nine Doors {2009-12-10} - 16.967 / 39.653
3DS Zero Escape: Virtue's Last Reward {2012-02-16} - 7.890 / 17.913
PSV Zero Escape: Virtue's Last Reward {2012-02-16} - 6.133 / 15.454
The numbers say it all, and I would be honestly surprised to hear VLR significantly (if at all) surpassed 999's sales in America.
Now, this would be a tough enough situation even if the series was just making a bit of profit. Even then, Spike Chunsoft has other franchises that are much more lucrative that they could be putting staff onto. I've long suspected (but have yet to check the staff lists) there's some crossover between the Dangan Ronpa and ZE teams, and it wouldn't surprise me if that's more true than ever with two DR games in development. DR also scratches that 'dark' itch like ZE, but in a much more marketable way.
But this isn't even a case of the series being only a little profitable in Japan. If it's straight-up in the red over there, that's not something the company's going to want to risk offsetting with Western sales. Obviously, I can't speak to Spike Chunsoft and Aksys' licensing, but it seems reasonable to assume SC sees less profit from a Western copy than from a Japanese one.
And as ShockingAlberto said, if Uchikoshi's considered Kickstarter and been rebuffed, it's likely because he knows the goal they'd need from there is too much. VLR was pretty close to full voice; that isn't cheap. 3D modeling isn't cheap. And while it's tempting to say, "just drop that and go back to silent sprites", that doesn't look good for Spike Chunsoft to downgrade the final entry in one of their series.
Finally, remember that 999 was re-released on iOS and Android last year. I wouldn't be surprised if that was also an attempt to recoup costs and show the series could be profitable in Japan. I'm guessing it didn't go very well.
I hope an answer is found - I loved the ZE games and have been eager for the third - but it doesn't seem likely.