While I get what you're saying, and this is an incredibly well thought out thread with fantastic points I agree with, this will all be moot with the NX. It will be successful on that console just because the nature of what a unified platform allows.
But to your three specific points, they're all true. To point 1, I really just think it's a matter of time before the presentation is improved. I think they just need the hardware with the right capability, and since I'm sure the NX will take a top down approach, developing for the console and scaling down for the handheld, they'll have more than enough power. After that, they just need to take presentational cues from games like Valkiria Chronicles and the'll have a fine looking game.
To Point 2, I think that'll just come with more success. I don't think there will ever be a day where the series is 100% VA'd, but you look at a game like SMT4 which did less than half as well and is adequately VA'd, so being on 3DS is definitely not an excuse. I think they just needed to be able to feel that the investment in more VA is worth it, but I'm sure it'll happen sooner rather than later. Also, Zelda should have full VA. No excuse.
To point 3, this is where I disagree. I don't think the gameplay is in any way less fitting on a console. I think it's just a niche genre. A lot of people, including me, just don't like SRPGs, regardless of platform. That doesn't mean it couldn't find success on consoles. People play strategy games on console and PC all the time. I don't see why this should be different from a gameplay POV. If you have the capacity to like this kind of game, you can like it anywhere.