From working around licensing issues all the time Seabass' explanation seems fine. They no-doubt bought the FIFPro license at the start of summer and that will probably run for a year which makes it difficult to change the rosters without breaching the terms of the agreement. Better play it safe. I liked Culo's idea though, although I'm not sure how it would effect the licensing issue. I don't mind doing a bit of editting on the game myself, but the only problem comes when giving commentary names to the players.
As for PES3 reaching the limits of the ps2. I feel they could probably squeeze a bit more out of it for a PES4. MGS3's graphics look great but how much of the EE is it using in drawing? The thing is that the AI involved in moving 21 players around a pitch, the motion of the ball, awareness of the players commands and the locations of everything as well as the rules of the game would probably take up a lot more processing power than the AI in MGS3, where you would probably have a maximum of 3 or 4 AI opponents on the screen at the same time. Therefore other resources which are used for the AI in PES3 can be used for the graphics in MGS3.
Now, on the xbox/ps2 issue I think the explanation given in the article posted by jumbo is quite good. The difference between the xbox and the ps2 isn't huge and the xbox hardly renders the ps2 obsolete by a long way. If you consider this analogy then... Think of your computer as a water system, the CPU is the pump that pushes the commands (water) down pipes which is the bus. Now, if you want to get more water to the 'customer', the common solution in computers is to increase the pressure in the pump. What the ps2's arcitecture has done is, instead of increasing pressure it has tried to widen the pipes. More water can pass through the pipes which means that you don't need as much pressure from the pump to get the same amount of water to it's destination. I don't know the figures but the fact that the ps2s CPU is 300MHz compared to the 700Mhz offered by the xbox is offset very well by the fact that you can transfer a lot more commands and data over the bus in less time than it would take for the xbox to achieve the same thing.
What we have really seen is that this 'new' architecture has taken time to learn to use effectively and efficiently. The xbox's architecture is that of an inextesible pc, games programmers have been programming on architecture like this for years and they therefore have the experience to get a lot out of the system from the get-go.