MCS is a requirement in permitted development regulations, so non-mcs systems would technically require planning permission.
You can't self certify the roof structure side of things just via the electrical registration with NIC.
An MCS cert or something similar is usually required by EPC assessors as evidence of what the system actually is - and EPC's are shortly to actually start using the MCS certs performance estimate rather than SAP. AFAIK there is nothing else similar to an MCS cert that can do the same job.
Most sub contract tenders spec an MCS certified system,
So for those reasons I'd recommend keeping up your MCS certification if you want to do a significant level of solar PV installation work next year, FIT or no FIT.