I have two questions to everyone specialized in Tokyo urbanistic.

1) We know that Tokyo has an high rise limit for buildings in the bay area (because Haneda airport). So why there are not high rise buildings in other city district? There is a limit in all the city? and if so, why there is a limit in district like shinjuku or chiyoda?

2) Tokyo urbanity looks to me really caotic and complex...different downtown and different kind of developments from a distric to another. So my question is: there is a general city development project for the city all or each district is free to plan an own project?

1a. Earthquakes.
1b. Land prices and ownership. Shinjuku was a former water treatment plant, so there was a huge area to build large footprint buildings like skyscrapers. Shiodome was a freight rail yard. Ikebukuro was a prison. To build in Shibuya or Ueno and you'd have to tear down tons of buildings and aquire a lot of land.

2. I think each ward has a development plan. Dunno about citywide.

Thanks a lot for the answers. Both were interesting!
I have just another doubt: I think Seoul and Taiwan have the same (or almost the same) earthquakes danger, so why they can build high-rise like Taipei 101 and Lotte tower?

It's not just the earthquake danger, but the type of ground the city has to deal with.

Thanks a lot for the answers. Both were interesting!
I have just another doubt: I think Seoul and Taiwan have the same (or almost the same) earthquakes danger, so why they can build high-rise like Taipei 101 and Lotte tower?

Taiwan has earthquakes, but not Korea.

Thanks a lot for the answers. Both were interesting!
I have just another doubt: I think Seoul and Taiwan have the same (or almost the same) earthquakes danger, so why they can build high-rise like Taipei 101 and Lotte tower?

Just to add to POS's response on Seoul's part, Seoul had the altitude limitation because of potential missile attacks and terrorism from NK. The limitation is going away tho.. I guess the similar could be true with Taipei in regards to China.

Thanks guys for all the informations.
So, if I have undertood well Japan has problem with the ground, the high price and earthquake as well (even Taiwan has the same problem).
But about the high price land I am little bit doubtful because the land price is the same if you build a 100 meter high building or a 400 meter skyscrapers, isnt'it?

According to this reserarch http://forum.skyscraperpage.com/showthread.php?t=81523 Minato-ku and Chiyoda-ku are the booming area.