I don't have a well defined opinion about 4-4-2 is dead (I do believe formation is not the real point), but I would like to point out one thing that you maybe want to consider in your positional thinking.
Millie and Cagiva already spoken about it in previous post, 4-4-2 as a formation without opposition is symmetric right? But when you pick your players and set roles, this is not symmetric anymore, because the guy on the left side of the midfield is maybe like Kuyt and has a great work ethic, work rate and is defensively concerned. If you have a C.Ronaldo or somebody like that on the opposite side, you are not "really" playing 4-4-2 anymore.
Another example before I start think about your dilemma, is the "between the line" positionning. If you had spend some time studying Brazil formation
http://www.zonalmarking.net/2010/03/03/analysing-brazils-fluid-system-at-close-quarters/
You have noticed that Robinho is neither acting like a pure winger nor a "forward", nor as a offensive midfielder. So Brazil is highly asymmetrical.
My point is, I do not think 4-4-2 is dead, I just believe more and more formations at top level are using asymetrical formation (meaning roles) to suit the skills of the players they line up. So whatever your board formation is actually, you can start the game with a 4-5-1 formation and actually play like a 4-4-2, you just have to adapt if you are outnumbered in the middle (@Xulu post), make a forward marking the DMC or something like that. You "just" have to know how to use your player in the best way and how to counter the opposition, how to associate your players (not exactly like england did with Lampard-Gerrard), how to create partnership
So at the end you have the question: universality/specialization. Like Crouchaldinho said, a 4 bands formation, 4-2-3-1 for example, is more likely to have "specialized" player in well defined role, but actually with the same XI, if you line up a 4-4-2, I insist with the same 11 "specialized" players, I don't think the opposite manager will be that troubled, he can be, but when you are in top level, you know how "specialized guy" are playing. For example, Makelele or Mascherano, in a 4-4-2 or a 4-5-1, you actually know the job this kind of players will have, and it doesn't matter because they are defensively oriented and almost every side have a back fours and at least a holding guy, so I go for "specialization". But if you look at the offensive guys, they must not be predictable, top players like Rooney, Ronaldo or Messi can play almost wherever on the field (I mean in an offensive way), but I you line up Crouch or Inzaghi you are predictable, and poacher are disappearing...I go for versatile players high on the pitch.
My point is finally, if you only have "specialized" player, whatever your formation is, you will be predictable. But I have some highly versatile players along 1 or 2 specialized one, and especially in the miedfield, it will be more difficult to know what to expect for the opposite manager. Even asymmetric formation with specialized players can be predictable, so just line up a very classic 4-4-2 or even a 4-5-1, the main informations I think come from your players and a bit for your line up. Dynamics formation (in defense and attack) are much more important than your starting formation.
In Fm, it could be harder to do such a thing, because formation states where your player will be, I am not sure but I think in an average way. So you have to use individual setting to really do what you actually want, but this is still limited if you want to be very accurate, knowing that most of people not really care about such possibilities.
So I agree with the previous post, just wanted to think more about specialization and universality, sorry if it is off topic, I don't think so, but just in case