SarusX,
I feel your pain.
You are not alone - far from it for everyone will meet with the same fate sooner or later if trying to make a serious game with FPSC and will be left with serious choices to make. Its unavoidable until and if improvements to the product are made.
I presume you are doing what you can to improve frame rates but its unlikely to be enough - you are unlikely to be able to overcome some of the fps issues in complex levels if you have them.
If you have done a great deal of work - I would keep backup copies separately to any you decide to drastically change in an attempt to improve fps and then perhaps at some future date if FPSC by some miracle should get a speed boost then you can bring the original level designs out of the cupboard so to speak and perhaps complete them.
I know what you suffer from - In my first game level alone I have around 30 fps constant except in a couple of serious lag spots at two lifts which for some reason kill the fps when I step into them and one spot where just one single active enemy knocks the fps badly.
Very frustrating for you I know.
Good luck with the project.