I may be wrong, so please correct me if possible. I think the license issue with PES and FIFA is more to do with the structure of the way they purchase/sign deals. The player likeliness is down to the FIFPro license and other licenses are signed with the Football associations and/or leagues. Therefore, the FIFPro licenses are available to countries that form part of it, so they can use it where possible.
Then again, some players have their own image rights, so that's another thing to think about.
PES and FIFA (I think) both have agreements with FIFpro, which is an organisation that manages the likenesses of players in things like videogames. Then they also have permissions from some individual clubs, or nations, or competitions. Football's easy in this regard because one licence gives you so much.
BLIC 2005 had an agreement with the ICC to use the World Cup and Champion's trophy (which allowed all players INSIDE those game-modes to have all the right players/kits etc, because that's the deal the ICC had with all those concerned).
Licensing's a very complex business.
Key thing to remember is that it's basically a promise from the person who has the rights to something that they will not sue you for using it.
You don't need a "license" to do ANYTHING with someone else's IP, but if you do not have one you take a risk that someone may think you are unfairly using it and attempt to get compensation. A court would then decide if compensation would be due.
Because of concepts like "fair use", it could be decided by a court that the accused party was in the wrong or it could be decided that they didn't gain anything unfairly. But obviously by that point there's a lot of legal fees and risk.
Great example recently:
EA Sports, CLC to settle lawsuits for $40 million -- source - ESPN
I'm sure that EA (and their LEGIONS of lawyers!) thought that they were in the right, and they were allowed to use those likenesses and names without having to pay for it, but the court decided otherwise.
A really simple example of this: I can put a picture of Natalie Portman on here pretty safely: she's probably not coming after me for that. But she *could* take me to court over it, as technically I didn't have permission. And if a court decided that I had benefitted from it, I'd lose.
Now, if I made a game "Natalie Portman Soccer 2013" and made a mint from it, it's *more* likely she would come after me, and that's pretty cut and dry: I profited off her name and she deserves compensation (the court would have to decide how much).
What I SHOULD have done is to get a written agreement up front which promised a certain amount of compensation for Natalie, and in return she would not sue me later on.
People think that a "license" costs money: but this is not always the case. Sometimes it promises a percentage of any profits, sometimes it's free (the other party might think that the benefit of appearing in the game is compensation enough: free publicity etc). And everything in between, all negotiated up front. Because basically your biggest worry is avoiding a nasty surprise later (if I slipped your likeness into a game without an official agreement (even if it WASN'T based on you and just looked a BIT like you!) you COULD get annoyed and sue me and I COULD lose.) But I assess the risk is low of that.
This all got rambly and may well be stuff people already know, but the question comes up a LOT. It just makes official a relationship and sets the terms: an agreement between two parties. You've signed hundreds of them yourself when installing PC software promising you will do this, and won't do this etc.