I found some links, after a quick Google search.
http://www.gameforms.com/news/?1164http://ff.warcry.com/#18008http://www.n-sider.com/newsview.php?type=day&date=2004-04-20#84Edit: For those who don't feel like clicking and reading, I'll stitch together and paraphrase some bits of it.
Square was thinking about releasing the Famicom versions of FF1 & FF2j as "Famicom Mini" series games, but decided to put the superior "remakes" on the GBA instead.
Nintendo specifically asked Square/Enix for a FF3j remake (Yay Nintendo!). Whether this was before or after Square/Enix thought about joining in on the Famicom Mini fun is unclear.
FF3j's mystery problems are still unexplained, but Square hasn't "abandoned" FF3j, and has still been working on the game (perhaps at a "back burner" level), and the problems may or may not have been worked out by now. They just weren't worked out in time for the Wonderswan or PSone.
A GBA version of FF3j "may be a possibility".
Takashi Tokita, the producer on these games, and the director of Chrono Trigger and Parasite Eve, says that he "could see himself" making an all-new game for the GBA (not specifically a FF game, apparently), instead of just non-stop ports/remakes.