Microkernels are not harder to debug than monolithic kernels. I'd even say that they are easier to debug, much easier. (Personal experience in debugging both.)
The problem with microkernel-based OSes is, as Linus Torvarlds aptly put it, that they turn well understood memory-protection problems into not-so-well-studied IPC problems. (The actual quote is «They push the problem space into communication, which is actually a much bigger and fundamental problem than the small problem they are purporting to fix.»)
The microkernel is not the real problem here, the big issue is debugging faulty IPC sequences between the servers that implement the OS services. A problem that is almost non-existent in monolithic kernel.
HOWEVER, current monolithic kernels are facing growth problems now because of two aspect: we want fancy remote storage accessed as easily as local storage (do you want to mmap a file stored in a RAID setup implemented with SATA-over-ethernet disks?) and the fact that the process model is too leaky and so we need stronger containers like VMs (that are becoming as much leaky abstractions as the current processes). All these new features require communication between various components that were previously though and implemented as independent. This means that the IPC problems are now creeping into the world of monolithic kernels.