Hmm...let me see...
Grandia Xtreme: The battle system was already quite solid and I rather enjoyed the dungeon crawling (which I rarely say about those game types). A remake would only need to tack on some of the stuff G3 added (like aerial combos), revamp/repolish the graphics, and get some better VAs. The story might've been weak but it wasn't too horrible, it was mostly the grating VAs that dragged it down. Granted touching up on the dialog here and there wouldn't hurt it one little bit.
Lunar 2: As I've said before, Lunar 1 gets waaaaaaay too much attention. Personally I thought L2 to be the superior game and if FF7 is supposed to be "so much better if they remade it with modern graphics" I bet L2 would be on par with such expectations. Especially if the battle system were revamped to be just a tad less repetitive. Either by enhancing it with more tactical depth or making it into a more action-RPG style battle system (Tales Franchise for example).
*cheating* Threads of Fate: Yes I know "technically" it's Square game but I'd like to mention it just because I'd like to see some other developer handle it. Square has...well...let's just say ever since FFX-2 my opinion of them has been steadily declining to the point where I have no expectations of them except for their inevitable demise. ToF I think should be remade in the hands of a developer more capable/responsible, especially considering the choices out there for handling stories that are both serious and comedic at the same time. To specify; I think ToF should be remade by either NIS or Atlus. As they both have shown the ability to produce fantastic games that know when to be funny, when to be serious, and how to skirt the edge of Japanese culture without being overbearingly fanservicey or stereotypical.
Legend of Legaia 2: Honestly, I've never beaten either Legaia Game. Something about them just lost me part of the way into them and I cannot specifically pin down what the problem was. Which was a shame as both games seemed to have rather decent potential. Legaia 2 in particular seemed to appeal to me more of the two so I would like to see it given a second chance. Maybe modernized graphics, an extended (and maybe not quite so cryptic) version of the Artes system would convince me to give it yet another shot.
Ar Tonelico: While it may not have been that long since the third game debuted; if there's any series out there that needs a second chance it's AT. A beautiful world, unique combat ideas (especially in the second game), the "potential" for decent character endings, AT basically has the framework of an amazing RPG...yet always seems to fail in overall execution. Whether its dumb as rocks protagonists, contrived and linear "dating scenes", gitch ridden programming, or strip-based gameplay, something major always seems to crop up in any version of AT that drives what should be a paragon of the RPG world into the cold dust. Take the concept and remove everything else, allow for more "free and meaningful" exploration of the cosmospheres, allow for moral style choices in the game (be nice to your Reyvatiel, or be a darker individual and force them to craft song magic at the expense of their sanity, ect.), keep the more creative battle ideas while chucking out the bad, and really, really, REALLY cut back on the meaningless fanservice.
Ephemeral Fantasia: Again another title I never really beat all the way but to this day I have a rather soft spot for it. I liked about half the cast and the story was rather interesting (for its time). The methods in which you recruited people, having to memorize events and think creatively to overcome the workings of fate, the integration of a musical game into the core mechanics of the RPG (take notes on how to do this Square instead of shoving out the drivel you are now), there was just so much to love about the game... Then of course you have the frustration of hunting down map pieces, getting lost for hours, too many random battles, a mildly frustrating skill system, characters who were utterly useless in combat,...ect. Polish this rock like your life depended on it and I think it could be sequel worthy. Not a diamond mind you but at least a ruby.
Orphen: Scion of Sorcery: One of the older games I will admit to having played, beaten, and honestly kinda liked. Sure the combat was janky, sure the dialog was weak in some places, sure the story wasn't ground breaking or amazing; but I did rather like Orphen. Heck the game got me curious enough about the source material that I hunted down and bought Orphen as my first anime box set ever. (Sadly the game seemed to be based more on the inferior second season.) While I'm not sure I'd want this exact game remade I think revisiting Orphen and including this game as like a "chapter" in a much larger project would be a decent investment of time. Especially if they rework some of the dialog and what not to put it more in line with what the source material's original season had to offer.
Popful Mail: I shouldn't like this as much as I do. Probably because the goofy fantasy hybrid thing reminds me of Slayers. But the VAs were actually pretty good, the music was catchy, the fights were challenging, and even though I never beat it all the way I found it to be a rather pleasant game to play. I'm amazed there was never any sequel or follow up. While it might be old hat as far as fantasy tales are concerned I think Popful Mail deserves at least one visit from the re-make fairy just to give it another chance to shine.