Scraped that… Mikoto will not be returning as the main lead after all, the one that got the 2nd season treatment is A Certain Magical Index… Toaru Majutsu no Index (とある魔術の禁書目録（インデックス）.
Which is not fair at all!!! No fair!!!
If you don’t know the differences… A certain scientific Railgun which my cute Mikoto is in, is an side story of the A Certain Magical Index, most notably that the whole 2nd arc of the manga features more Mikoto and her clone sister than Index, which is almost non-existent. Mikoto’s story then came alive on it’s own starting with the manga… which is quite different from the anime… I must say.
Either way, this series will only be out at least 2 seasons from now… since this is only the announcement of it starting production.
BTW, there will also be PSP Index game… suggesting a release in winter 2010…
Source: Sankaku Complex