I think both games are on the right consoles. Ocarina of Time would have nothing to gain from being on the Wii U besides HD visuals (which isn't enough of a reason), whereas The Wind Waker would have things to lose from being on the 3DS.
The Wind Waker is a grand adventure, pure and simple. The scale of the world, the size of the adventure, the openess of The Great Sea, these are all things which benefit from having a big screen with a wide field of view. No other Zelda game captures the excitement of exploration better than The Wind Waker and confining it to a handheld would be to confine the feeling of the adventure. Ocarina of Time doesn't have this issue. The overworld is so much smaller and the areas are so much more restrictive or closed-in that being put on a smaller screen doesn't really have much of an impact on how exciting it is. In addition to that, The Wind Waker's plot is driven by actual exploration, the need to go out into the wide world and find the things you need. Ocarina of Time's is driven more by specific events and being told where to go next. The nature of these games is very different: one is very open and free and benefits from being on a much larger screen; the other is closed and small and doesn't have to sacrifice anything by being on a smaller screen.
Then there's the nature of portability. Ocarina of Time, having a more defined and structured overworld and following simple, clear goals, lends itself better to being played for short periods of time. The game is much easier to break into 'chunks' of gameplay and this makes it easier to apply the short time of a bus journey, or a lunch hour, or a car ride to achieving specific goals within it. The Wind Waker's structure and design is very different. The overworld is not as clearly defined, making it easy to get lost wihtout a map, and the objectives are not as clear as they are in Ocarina of Time, most notably the Triforce Hunt which leaves you to figure things out on your own. There is also the distraction factor, the liklihood of players seeing something odd or interesting while on the open sea and taking time out to go and see what's there. The game has more secrets and more hidden items than Ocarina of Time and so even simple objectives can take a lot longer to complete as players deviate from their course more often. This makes the game much less adaptable to a portable device as people will find themselves having to cut things short because their train has arrived or their free period is over.
Going back to the map for a second, the function of the map is so much more central to the gameplay of The Wind Waker. Navigating on The Great Sea is very difficult without a detailed sea chart, something the game itself takes pains to remind you of. Having that sea chart in your hands in the form of a dedicated screen separate from everything else is a huge help, as well as drawing you in to the world by, well, putting your map in your hands. Ocarina of Time doesn't make any significant use of maps and so it doesn't sacrifice anything by displaying it on a small screen. The Wind Waker's sea chart would be cumbersome if it were on such a small screen, making the game a better fit to the Wii U.
As for the visuals, I have to disagree with the apparent consensus. Ocarina of Time doesn't really have anything to gain from HD. To be honest, nothing really does. A visual overhaul can be an important factor in a full remake like 2002's Resident Evil, but for one of these 'half-remakes' that don't change the structure or design of the game in any way what's the point beyond looking pretty? The Wind Waker looks a lot nicer with the upgrade, and Ocarina of Time would even moreso because it lacks the almost timeless art style of the former, but neither game really benefits from HD beyond being easier on the eye. Where visuals do make a more significant difference is in 3D. 3D makes the game world feel more like a real place. Seeing Hyrule in actual 3D draws you into it a lot more and gives a sense of reality, like you can reach out and touch it. Ocarina of Time 3D is arguably a more visually appealing game than The Wind Waker HD because of this. Seeing as The Wind Waker's world is a vast ocean with small islands littered about, you would only really see the benefit of 3D in dungeons or on a few notable islands, like Windfall or Dragon Roost. Overall, the 3D effect would be wasted on the odd splash of water or seagull flying by. Nice effects, I'm sure, but the tighter world of Ocarina of Time can dazzle us with the 3D effect in pretty much any area of the game. It's a denser world, visually, and that is where the 3D thrives. For an example, just go into any of the houses in Kakariko Village or Hyrule Market. Heck, just step out onto Link's balcony in the Kokiri Forest. The effect is immediately noticable and has a bigger impact than the nice lighting in The Wind Waker.
The other changes each game received, such as the more intuitive inventory systems, gyro control for certain items, and other streamlining tweaks (e.g., Iron Boots being an item, not gear; the swift sail) are things that could and were done on both 3DS and Wii U, so neither title would lack any of those general gameplay improvements if they were switched. However, The Wind Waker would perhaps have lacked the Tingle Bottle that enabled its fantastic Miiverse integration. Finding messages in bottles on The Wind Waker's coastlines and floating in the sea fit seamlessly into the pirate/seafaring fantasy of the game and provides a practical function of allowing players to share pictographs for use in the Nintendo Gallery sidequest, opening up a part of the game many fans ignored originally because of how laborious it was. There isn't really anything Ocarina of Time stands to gain from Miiverse integration, and it would be harder to include it in a way that was entirely consistent with the game's theme as they did in The Wind Waker.
Ocarina of Time has nothing to gain from being on Wii U except a new coat of superficial paint. The only reason I can think for why people would have preferred Ocarina of Time HD is because they simply like the game better. The Wind Waker would have to sacrifice a lot of what made it feel special, as well as some significant and worthwhile mechanics, if it were to be confined on the tiny 3DS. The Wii U is a far better home for it and I am very glad these games were released on the consoles they were: the most appropriate ones.