SC-FDMA disadvantages
Some more disadvantages:


Channel estimation using pilots is harder, because you do not have orthogonal data on each frequency bin, compared to OFDM. That's why e.g. LTE uplink resorts to a midamble for channel estimation in uplink
Application of non-linear MIMO detection algorithms is harder (i.e. more complex), because you essentially have coupled MxM elements from each transmit antenna, compared to 1x1 elements when using OFDM.
In high SNR regions I think SC-FDMA does not perform as good as OFDM when considering a coded transmission with linear detectors.


Regarding the data loss: Even if $M&lt;N$, there is no real loss, because the used bandwidth of your signal is only M frequency bins (ignoring any guard carriers). So, any other system can use the remaining N-M frequency bins.