It's unquestionable that federation and decentralisation increase complexity significantly. For context, prior to Matrix the Matrix team used to write commercial comms app silos for telcos - and then we had the epiphany that building silos is harmful to end-users and the industry as a whole, and shifted entirely to the longer-term mission to build an entirely decentralised & open alternative. Despite the fact that we already had an entirely functional centralised implementation, it took about 1.5x longer to create Matrix. And if had been starting from an entirely clean slate, I suspect it'd have been 3-4x longer.
However, we very strongly feel that the resulting freedom and choice from the resulting open ecosystem is worth the additional complexity.
Users can choose any service provider without compromising interoperability. They can run their own servers. They can write their own clients. They can write their own servers. They can choose precisely who they trust with their data. They can contribute to the spec and help define the ecosystem. They aren't forced into trusting a provider who may be trustworthy today, but who knows in future.
I believe Moxie's viewpoint is that privacy is paramount, and any complexity which could introduce bugs which could undermine security/privacy is anathema. From a cryptography dev perspective, this makes perfect sense.
On the other hand, Matrix believes that there is more to life than just privacy, though (as critical as privacy is, of course) - and it is possible to have both privacy and freedom.
Yes, it slows down the rate of development a bit. Yes, it means you have to think much more carefully about layering the protocol to allow the different layers to evolve as independently and efficiently as possible, with the necessary mechanisms (both technical and organisational) to upgrade and lock out obsolete clients and servers. Yes, it means there's more complexity, where bugs could hide. Yes, it means that you may not be able to force the world to upgrade as rapidly as a silo might in the face of a critical security issue.
However, we think it's worth it.