It shouldn't be a problem as long as your fuel trims are actually adding enough fuel... if you are maxing out your fuel trims and it is still too lean then it could definitely be a problem.
Do you have a wideband o2 sensor that you can use to compare the reading of your stock o2 sensor to?
The "System too lean" code is set because your fuel trims have stayed positive over a long enough period of time to set the code, the possible reasons for this code to pop up are either:
1. Your car is too lean because of un-metered air entering the intake tract after the MAF sensor
2. Your car isn't getting enough fuel (could be low fuel pressure, bad injector, etc.)
3. Your o2 sensor is going bad- if it thinks the air/fuel ratio's are too lean it tells your ECU to inject more fuel (fuel trims), but if the mixture really isn't too lean, say it's actually good, or too rich, and the sensor keeps reading that it is too lean it will keep telling the ECU to inject more and more fuel.
I've seen a truck that was injecting so much fuel that it was literally raining black soot when the engine running (the truck had stacks like a semi

)