From: Near Portland, OR
The game has to bring new units onto the map. All units have a base where they will appear. However, if that base is not in friendly hands when the unit is scheduled to appear, there is always a secondary arrival location. I believe it's the national home base for all nationalities. For the US it is San Francisco for example. For Japan, it's Tokyo.
I believe a fair number of units arrive in Tokyo anyway. In a game against the AI, units can end up piling up in Tokyo, especially if you have done a lot of damage to the Japanese merchant fleet. The AI would like to move units to various outposts, but if it can't find suitable transport, the unit will sit where it arrived.
So against the AI, Tokyo can end up with a staggering stack of units, both air and land. Especially if you're ahead of the Allied real world time table (a lot of units that were supposed to appear in various remote bases will find the base has already fallen when the arrival date comes around and will divert to Tokyo).
It's not really any nefarious plan to make Tokyo hard to capture, it's just a consequence of the game engine and the AI trying to do the best it can with a war that has turned out very differently than history.
WitP AE - Test team lead, programmer