A “high-level” employee at Research In Motion (RIM) today published an anonymous open letter that criticizes the BlackBerry maker for its shortcomings in recent years. The letter was published with Boy Genius Report, which said it had confirmed the identity of the letter’s author.

The letter takes aim at everything from management to the BlackBerry products themselves and even goes so far as to say that RIM has fallen behind Apple.

 “We often make product decisions based on strategic alignment, partner requests or even legal advice — the end user doesn’t care,” the author laments. “We simply have to admit that Apple is nailing this and it is one of the reasons they have people lining up overnight at stores around the world, and products sold out for months,” the person wrote, adding that RIM has “a great opportunity to build something new and “uniquely BlackBerry” with the QNX platform.”

The letter goes on to suggest that RIM needs some serious help in the software department, suggesting the company acquire some “heavy hitters” for its software management team. “Look at our software leadership teams in terms of what they have delivered and their past experience prior to RIM… It says everything,” reads the letter.”

The author also takes aim at RIM’s lack of advertising and marketing, the company’s habit of lashing out at the media for criticisms leveled at the company, as well as lack of sophisticated apps for its devices. The author suggests that overconfidence might be at least part of the problem. 

“Overconfidence clouds good decision-making. We missed not boldly reacting to the threat of iPhone when we saw it in January over four years ago. We laughed and said they are trying to put a computer on a phone, that it won’t work,” wrote the author. “We should have made the QNX-like transition then. We are now 3-4 years too late. That is the painful truth… it was a major strategic oversight and we know who is responsible.”

RIM responded to the letter, with a post at the Official BlackBerry Blog, dismissing it as a possible fake, saying that a high-level executive in good standing with the company would not voice his concerns in an anonymous letter. Still, the company did acknowledge the letter to some degree.

“Regardless of whether the letter is real, fake, exaggerated or written with ulterior motivations, it is fair to say that the senior management team at RIM is nonetheless fully aware of and aggressively addressing both the company’s challenges and its opportunities,” RIM said.

At the behest of investor pressure, RIM announced yesterday that it would assess it management structure .  The company has received criticism in recent months that co-CEOs Jim Balsillie and Mike Lazaridis have not shown enough accountability for the company’s decline.

RIM also yesterday bowed to pressure from shareholders to examine its current management structure. The company came to an agreement with Northwest & Ethical Investments (NEI), which holds large investments in RIM, to withdraw a NEI proposal that asked RIM’s board of directors to adopt a policy that divides the role of Chair and CEO, and that RIM have an independent Chair.

RIM announced yesterday that in return for withdrawing the proposal, RIM’s board will establish a Committee of independent directors whose mandate will generally be to “(i) study the appropriate balance between an independent lead director or chair with full and exclusive authority customarily held by such an office holder, (ii) determine the business necessity for RIM’s Co-CEOS to have significant Board level titles to assist their selling and other responsibilities with certain large customers in overseas markets, and (iii)  propose and provide a rationale for a recommended governance structure for RIM, which will include clarifications of the Co-CEOs and Chair roles, as well as the Board’s mandate.”

The Committee will consult with NEI Investments in developing the specific terms of reference for this mandate and before it issues its report by January 31, 2012. The Board will publicly respond to the recommendations of the Committee within 30 days.