@ Squilliam
Or the game engine they have to work with and adapt (for example other people's code) or usage of middleware technology which still hasn't been adapted enough (the developers being far more dependent on 3rd party coders).
Lots of info can be found on CellPerformance.com, it's not as easy as a simple recompile for the SPEs.
Of course they intend to use as much as possible over time, but redesign takes time and effort. They are still using only 4 SPEs but they moved a lot of workload from the PPE onto these SPEs, so they are using more processor time on these SPEs than they did before. It could well be Killzone 2 when it is released uses all 6 SPEs, but the SPEs will have a lot of processor time to spare. Rome wasn't build in a day.
Adding additional effects or onscreen activity for Killzone 3, taking more GPU workload off the RSX to improve framerates, take more workload from the PPE onto the SPEs for performance gains, etc.