Animal Crossing U: Very possible. One of the probable early(?) 2016 games for Wii U. I think we'll get a trailer for that.
Amiibos: They'll appear in some capacity. Maybe not even in the digital event. More smash waves will get announced, more new series, new games that will support them... Oh and there will be an apology for the mess they are.
Devil's Third: Is this game still alive? If it is, then it probably get a trailer. Nothing more,nothing less. I guess it's coming this year, if it's still alive of course.... Seriously, this got announced weirdly and we hardly heard anything for it since last E3.
Donkey Kong U: Too soon, not happening.
F-Zero U: Not happening.
GameCube VC: Eventually this will happen, but i doubt it will be on E3. Maybe just an announcement for the future. I mean, they announced Wii, DS and N64 but still there are only a few of them on their shop. Also, I'm not sure what would they release there right now. Wind Waker had the HD remake recently and the Prime games got Trilogy. The other really big games I can think are Sunshine and Luigi's Mansion but I doubt they would be enough. Stuff like Melee or Mario Kart wouldn't work greatly. It still could get released though, with the 2 Mario games I mentioned and maybe more coming later.
Illusory Revelations #FE: Trailer, new info, maybe a more specific release window. Hyped about the game.
Kirby U: Too soon I think.
Mario U: I think this was rumored or was confirmed to exist. I think it was stated to be a 3D Mario, so I really hope it's a Super Mario Galaxy 3 or something similar. Considering that Mario Maker is on the way too, another 2D Mario won't happen for some time. I think an announcement during the World Tournament would be really neat but I'm probably just optimistic.
Mario Sports Something: This will happen probably... At least I hope it's something good like Strikers.
Metroid U: My dream game for E3 and I think that it's not really far-fetched. The series isn't dead, just dormant and an announcement would make sense to happen in E3, not just on a regular Direct. My only fear is what exactly it will be. A Prime like game? A Metroid Other M-like game? Maybe a 2D one?(hopefully not) If it's happening, it won't come this year, sadly.
New IP: I have no idea what this could be. Last year we got Splatoon, I didn't see that coming. I'm sure that they're release something new but maybe it's not something big. Maybe even smaller like Splatoon. Either way, we'll see.
Paper Mario U: Rumored too. Quite possible too, with a 2015 release date. Hopefully more like the first two games, rather than the Wii or the 3DS one.
Pokken: I don't really believe that this will be announced for Wii U so soon. I think it's expected to come but not now. A 2016 or even a 2017 release, and it'll probably be confirmed for Wii U sometime after its arcade launch.
Remake: I believe(and maybe I'm a minority), that their releases for late 2015 are somewhat scarce now. So what's better than an easy to make, remake? If they announce the NGC support for VC, this may not happen though. A good candidate would be Twilight Princess.
StarFox U: Probably one of their big games. This will be demoed, have a big trailer, many interviews with Miyamoto and other developers later... Generally it will be their flagship game this E3. Guard and Big Robot will be part of it. Even though I don't really like the series, I'm kinda hyped for what this will turn out.
Smash DLC: Optimistic about it. They'll probably announce a new character around the middle of the Event. Maybe even a second, returning one but we already have Ness.
Splatoon DLC: Considering that the game will be out for quite a few days before E3, if they plan to release DLC for this, this would be a nice time to announce it. Maybe they're even release some free update around E3. Generally, I'm certain they'll mention the game in their Digital Event.
Surprise Announcement: Either the new IP or a surprise collaboration for exclusive third party game.
Xenoblade X: I guess this will appear too, but not much to see as it's already out in Japan. A (cinematic?) trailer and it will get announced for late Summer/early Fall.
Yarn Yoshi: I guess this is bound to appear too, despite coming really soon. A launch trailer and maybe some kind of announcement for DLC, but I doubt that.
Zelda U: I doubt we'll learn nothing new about this. I get it, no trailer, no playable demo but I believe we'll get new info on some capacity. Probably Aonuma confirming things or maybe another sneak peek.
My thoughts about Wii U... We'll probably get some 3rd party announcements too, like maybe Black Ops 3, but not much. Oh and an indie sizzle reel. Hmm, most of them are pretty realistic I think but perhaps not all of them will happen. I hope there will be something that I don't expect on their event...
Edit: The post is kinda big, sorry about the bold too...