That Sankei article is incorrect -- non-Japanese residents registered for the automated gate program must still be manually approved by an immigration agent. Therefore, it would be a vast improvement if they simply eliminated the requirement to submit the immigration form and made the process truly automated. As with many things in Japan, I expect any movement towards this to be met with strong resistance from anti-immigration conservatives.

Edit: Sorry, the Sankei article was describing the future "Trusted Traveler" system. However, if it resembles the current system, it will still be inadequate.