You have a point but Square Enix doesn't usually leave V out when they do something with VI. Same situation with I & II.
I think Nintendo would want to target FFVI as it would have the most impact and makes the most sense. When people think about the best SNES games, FFVI is always high on so many people's list. For those who grew up during the SNES era, it was a very memorable and epic experience. When you talk about SNES, FFVI comes up a lot.
When people think Final Fantasy, they mostly associate the IP with Sony and the PlayStation, but that's mostly FFVII and above and not so much the first six titles.
So if Nintendo were to target a mainline Final Fantasy game, they don't really have many options. They don't really have a strong history with FFVII and above so it makes no sense to get those titles. It would probably be very hard to do so as well because Square Enix will not ignore Sony and the PlayStation platform. Meaning, if Nintendo wanted a FFVII exclusive remake, chances are that it would not happen. It'd have to be multiplatform at most. Final Fantasy fanbase is currently on Sony platforms.
The only mainline titles Nintendo does have a strong history with are FFI, FFIV and FFVI as those were the only three titles that had a worldwide release when they were originally released. There's no point revisiting FFI as there's not really much going on with that game. It's pretty straight forward and doesn't have much of a deep story or anything. FFIV has already been tackled with a 3D remake on NDS and a downloadable sequel on Wii. That leaves us with FFVI, which has received an ugly iOS sprite remake.
So yeah... I think FFVI makes the most sense. When I think about it, FFVI is right in the middle of things. It's associated with a group of mainline Final Fantasy titles many fans don't talk much about (FFI-FFV) but it's right on the edge of being part of that group most fans do talk about (FFVII and beyond). All it really needs is a big push and the only way to do that I think would be a proper 3D remake but not something like we got with FFIV on the NDS. If Nintendo wants to make some noise with the Final Fantasy fanbase, FFVI makes the most sense to target.
Side note: I kinda wonder why Nintendo doesn't try and target Chrono Trigger? Original release was on SNES after all and is considered to be one of the best games for the platform. Hell, it's up there with some of the best games of all time and nobody really talks negatively about it. If Nintendo were going back in time and looking for 3rd party IPs that they could help revive, Chrono should definitely be one of them.
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