I actually looked at the WoW armory for their guild before episode 3 went live, so I knew that Cox was going to make a guest appearance, and that they'd fail the challenge miserably (and they apparently haven't touched it since that show was filmed). I was expecting a train wreck, but not THAT much of a train wreck (I've ran the dungeon that they ran several times across multiple characters, and have never had anywhere near as many issues as they had, even when placed with random players). Although it did put things into perspective a bit for me (You kind of forget about learning curves once you've played for well over 10,000 hours), and made me remember that just dicking around with friends could be just fun as actually playing the game.
Honestly, I think that the main reason why the reaction to Nintendo's presentation was so negative is because of how high expectations for Nintendo are nowadays. The past few years, Nintendo has done an amazing job with their E3s, easily being the best in show (or close to it). This one had a strong start, but tapered afterwards. The things I can see as possible issues:
1. The Muppet skit theme was a shadow of the Robot Chicken skit theme of last year. Felt like it didn't reach its full potential (no pun intended).
2. Animal Crossing being a Mario Party clone, rather than a mainline AC title for the Wii U.
3. The Metroid debacle, as you mentioned.
4. Amiibo functionality out the wazoo (it doesn't help that the amount of paid DLC from the Smash direct left a bit of a sour taste in the mouths of some)
4. The "Let's Super Mario" ending (I wonder if they'll allow MADs/YTPMVs?)
The other things that immediately come to mind are more minor nitpicks. Overall, not as great as previous years, but Mario Maker still looks fun as hell, as does the M&L/PM crossover (although I've heard that both series have gone downhill a bit as of late). And getting a Mother localization gives me a sliver of hope that we'll get Mother 3 down the road please don't burn me alive, Reggie.
Noice. It honestly feels like the time between the end of last season and the beginning of this season is much longer than it actually is. Which is odd, since I've mostly ignored pony-related media this time around.
Interesting. Unfortunately, it looks like F2P is heavily restricted still, so I'll pass on paying months for more than 1 MMO. To that end, I still have rather fond memories of Runescape back in the day (I played from 05-early 06). Despite how outdated the grinding-heavy system is at this point, I still have to give credit for the world still feeling like, well, a world. Like, how some certain merchant types are exclusive to certain towns, and commonplace things aren't in every town. It feels like a style that's seldom seen in MMOs nowadays. Similarly, the quest system still is one of the finest to this day, and 07scape has some criminally underrated music.