Mercury News reports that third party developer and publisher, Electronic Arts’ underestimation of the Nintendo Wii could eventually come back to haunt the firm as it struggles to support the platform with the same gusto as it has the Sony PlayStation 3 and Microsoft Xbox 360.

“This transition does seem to be a bit more painful for EA,” said Todd Greenwald, financial analyst with Nollenberger Capital Partners, who also believes EA will continue to reign supreme amongst the gaggle of other top third-party software publishers, including the likes of Ubisoft and Activision.

However, other analysts and investors are beginning to question Greenwald’s opinion, particularly since EA’s rise to the position position as third party market leader was no coincidence after it supported the PlayStation 1 and PlayStation 2 so doggedly.

“It has huge implications,” said one anonymous industry consultant. “Nintendo will return to its historical position as the No. 1 hardware and software vendor and will leave everyone else fighting for second place. “EA now needs to adapt but analysts say this will be difficult due to the company’s size.”

Further analysts suggest that EA now needs to change how it operates its development process in order to adapt to what may become a Nintendo-dominated gaming world, one saying that the “challenge is it’s such a big ship. How do they navigate the water quickly?” EA officials have blamed the recent problems on the complexity of the transition.

We have reported previously about EA’s hurried attempts to shift some of their sizeable weight behind the Nintendo Wii after the company’s initial (and not unfounded) speculation over the console. The likes of The Godfather: Blackhand Edition, Madden NFL 2007 and Tiger Woods PGA Tour 2007 are testament to their first batch of efforts. It’ll be interesting to see how their alliance with Nintendo’s latest machine develops over the coming year or two. Watch this space!