It's got absolutely nothing to do with how difficult or easy microlights are to fly. I fly both microlights, as well as fixed wing aircraft, and there's absolutely no difference, apart from the fact that microlights are weather dependant and fly much slower. They are aircraft. The fact that one requires a minimum of 25 hours to get an MPL, as opposed to 45 hours for a PPL, might contribute to the problem. Whether it's an MPL, or a PPL, one requires a radio licence which teaches these basic skills.
One cannot enter the CTR without permission, and a transponder. If it wasn't a serious issue, then there wouldn't have been a CTR.
It is without doubt a very serious issue. What's next? Microlights in the TMA?