What do you guys think are common misconceptions or overrated attractions in Tokyo?
Here's some ideas to get the topic started:
You can use the jr pass for getting around Tokyo
The JR pass isn't so useful in Tokyo as it's only valid on JR lines. Whilst the Narita Express from Nartia to Tokyo is JR, pretty much any other journey around Tokyo will involve using non-JR lines, plus it's not very good value using any of your JR pass days to make short journeys across Tokyo - best to activate your JR pass when you are making Shinkansen journeys between cities.
Also note - there's no useful day pass ticket for Tokyo. Whilst each train company sells a day pass, they are all but useless because you'll inevitably need to cross to a different line and pay extra anyway. The only thing you need to know about train tickets in Tokyo is buy a Suica (or Pasmo) IC card and use that - more on transport around Tokyo here.
Tsukiji is the best place to eat sushi
Looking for the best sushi in Japan is a bit like looking for the best espresso in Italy, or best pad thai in Thailand - it's something that's good almost everywhere in the country. If you've not eaten sushi in Japan before, then you'll probably find even the cheapest kaiten sushi will taste amazing compared to your experience so far, so don't worry too much about getting the "best sushi" experience. Moreover fresh fish from Tsukiji is delivered all across the city every day, and most of the highest regarded restaurants aren't in Tsukiji itself anyway (a lot of them are in near by Ginza).
That being said, Tsukiji market is an interesting destination in itself (plus it's going to be permanently closed soon) so it's certainly a good place to visit. Bonus idea - try buying some tuna and have a DIY or Make your own breakfast, see our very own Greg Lane doing this here.
Jiro Sukiyabashi is the best place to eat sushi
Similar to above, there's plenty of really exceptional options and the one place that made it on to Western cinema screens is just one of dozens of high-end sushi eateries in Ginza alone (for example the popular food rating site tabelog lists Jiro at #9 for Ginza). Plus you're unlikely to easily get a reservation (unless like many people on trip advisor you end up going to his son's place in Roppongi and thinking it's the world famous Jiro dreams of Sushi).
Obviously the whole point of Tokyo Cheapo is to show the world Tokyo is not nearly as expensive as its (outdated) reputation. It really isn't pricey especially if you find some cheaper accomodation, don't use taxis for anything more than 2-3km, eat local food and do some of the numerous cheap/free activities.
And some common "tourist traps"
Mount Fuji - Mount Fuji is the tallest and most striking mountain in Japan, however it's so popular climbing has become more of a queue than a hike. Plus the climbing season is just a few weeks in Summer and you can't see how amazing Fuji looks when you're on it, instead for the spectacular view climb a near by mountain (or indeed one of the many other thousands of mountains in Japan).
Robot Restaurant - whilst everyone I know who's been has enjoyed it, make no mistake it's a recently built attraction purely for tourists - there's nothing authentic about it and you won't find many Japanese people in the audience (that aren't accompanying foreign visitors).
Tokyo Skytree - It's a super tall tower with an amazing view, and also amazing queues. There's some (albeit not as high) view points that are cheaper or free with less queuing involved, namely the Tokyo Metropolitan Government Tower in Shinjuku, and the Mori tower (Roppongi Hills).