Multiple Index Templates - Custom Analyzers

In 2.x I would maintain my index settings in one template, and the individual mappings in seperate templates. But now in 5.0, when creating these individual mapping templates, it's throwing errors saying it can't find my custom analyzers (that are defined in the seperate template).

Has something changed, perhaps where templates are now more rigorously validated at template creation time rather than index creation time?

Yes, in 2.4 and 5.0, we validate each template as a complete mapping and settings.

And we are thinking to improve the validation of template

Hmm, looks fairly contentious. I agree with the sentiment though that this is a undocumented breaking change, and it's disappointing this use case wasn't considered.