I agree with all that has been stated about the negative aspects of the IF. However, the REALITY is that the uninitiated, such as a Committe judging tenure, or a Committee deciding on a new Chair appointment, absolutely require Impact Factors for each article.
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Therefore there is no use in arguing against the importance or lack of same of the IF.....lets just get it.
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Scientists (sad but true) belong to the most conservative professionals in general. Despite anything that is counting agaist the IF, this will remain the measure for 99% of us for time to come.
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Authors will still care about it, although they will officially say that IF's are ridiculuous. But scientists are hypocrits (like most people) and they will continue to send their papers to high-IF journals, whether we like it or not.
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I say this with some sadness, because I myself do not care much about IF:s, but I know a terrible lot who does and I have given up all my attempts to discuss this with people, since it seems hopeless to argue about. That's human nature, I guess.
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People are still quite concerned about IF:s, although they admit that they are misleading, but as long as the research finance system favours authors who publish articles in high-IF journals, they will continue to try get published there, whether we like it or not.
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I couldn't agree more with all that is being said about IFs. Unfortunately, the reality for most academics is that all kinds of evaluation committees use IFs to evaluate a researcher's output.
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I know how flawed IF is, but we just cannot be blind to the reality and should still make a best effort to have PLoS ONE indexed by Thomson.
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The reasons you enumerate against the IF system are of course valid. However, IFs are still the most used way of evaluating a researcher's career and value. Even if we find this ridiculous, it's just the way it is. Therefore, I find it very important for PLoS ONE to try to get an IF, independently of the other suggestions that have been made.