The scope of FF6 was way beyond FF4. But even aside from that, the fact SE say it'd cost so much and take so long are to me indications they do want to do right by it. They know they couldn't maintain the scope of FF7 with the graphical quality of XIII without a budget, and time frame that make it completely impossible.FFVI would be similar to FFIII and FFIV in terms of budget and level of changes, I'd imagine. As it is clear from the comments from SquareEnix, the problem they have with FFVII is the budget would be huge. This already indicates to me they have the wrong idea about the scale of the project relative to the handheld remakes.
They do have options, they don't have to do it on PS360 firstly. PSV/3DS would be considerably cheaper. They don't have to do it full 3D behind the character style, they can keep it top down, fixed camera etc.
It's always going to be a major project, but again, look at FF4, they did a sequel, they did an interquel too, both crap, neither affected how they presented 4. Despite the sins they may have committed elsewhere for that game, the product itself remained of high quality and true to the source material.