It is possible to build N-point FFT using two N/2 point FFT. But it requires extra steps and it is not straight forward. For example for 1024 point FFT with 128 inputs, you use two 512 point FFT, each of them with 64 inputs. You need to split the inputs to even and odd samples. Then you need to combine the outputs of the FFTs. The even samples is basically the sum of two FFTs. But for the odd sample you need to run circular convolution. This step requires a lot of hardware.
I would like to understand your use case. Remember that with 64 inputs and running at 250MZ (on Xilinx Virtex 6), the throughput will be 16 Giga sample per second. Does your application require higher throughput?
Note that increasing the input vector size, make it harder for FPGA to route the signals. For some of the devices you may not be able to route the signals, and for other devices it will affect the maximum processing clock rate.
