A few thoughts that may be behind this: Li-ion accumulators age faster when they are fully charged. The phone manufacturers face a dilemma here. If they always charge the accumulator to only 90%, it lives a lot longer, but of course has only a reduced capacity, namely 90%. If they always charge it up to 100%, they face two problems:
Charging a Li-ion accumulator fully takes a long time, because the charge current has to be gradually reduced to avoid damaging the accumulator.
Even with the reduced charging current the accumulator is strained by charging it fully.
The currently widely adopted compromise is to show green at 90%, inducing many users to disconnect the phone from the charger and thereby extend the lifetime of the battery. If the user keeps charging the phone in spite of the green light, the battery is slowly charged up to 100%. This is sensible if you need the phone a lot during the coming day, but it does age the accumulator somewhat.
I think this is a good solution. Several phone types work that way, such as the Google Nexus One and probably many others.