A major factor is certainly the technological evolution: some of today's microlights perform better than the average spamcan, looking better and costing less, in maintenance and fuel, though not in acquisition. For a single person flying VFR, or two with little if any luggage, there is little reason to fly a certified aircraft today.
Reasons I can see for keeping to certified planes: IFR , more than two persons, luggage.
A lot of craft, registered today as microlights, should really be called LSA's, and I wonder if they'd still be as attractive - lower fuel cost remains, but maintenance can no longer be done "at home" so will be significantly more expensive.
Another factor not yet mentioned is delocalisation: the Belgian civil register is indeed draining fast, but a lot of that is to neighbour countries. Of the Belgian based microlights, I reckon at least half are French registered, while Belgian glider operators are massively switching to the German register.
But, for all I understand about EASA and what they try to achieve and how, I can only be happy they are not (or not yet?) meddling with microlights and gliders. Balloons neither, I think.