On to your questions.
1) Choose languages that developers are familiar with, not the best tool for the job
How familiar developers are with the language is part of what determines what is best for the job at hand in a real organization.
It isn't the only factor. For example if you're doing something new (to you), doing it in the language that you find wherever you are learning it from makes sense because you'll be more likely to get help through complex issues.
That said, do not underestimate the support advantage of using a consistent toolset that everyone understands.
2) Avoid microservices where possible, the operational cost considering devops is just immense
See https://martinfowler.com/bliki/MonolithFirst.html for emphatic support.
If you go the microservices route, think ahead about predictable challenges with debugging failures 3 calls deep, and plan in advance for monitoring etc tooling to solve it.
3) Advanced reliability / redundancy even in critical systems ironically seems to causes more downtime than it prevents due to the introduction of complexity to dev & devops.
As the old saying goes, DBAs are the primary cause of databases going down. Reliability is not something that you just plaster on top blindly. An systems are good at finding failure modes that you never thought of.
4) Continuous integration seems to be a plaster on the problem of complex devops introduced by microservices.
No. Continuous integration is actually a fix for developers checking in clearly broken code and then nobody discovering it later. That said, it does little good without a number of other good practices that are easy to ignore.
5) Agile "methodology" when used as anything but a tool to solve specific, discrete, communications issues is really problematic
This one generated the most discussion. I would say sort of, but you went too far.
Any set of poorly understood principles, dogmatically applied, is going to work out badly. Agile is actually a set of good principles that addressed a major problem in the common wisdom back in the day. But the pendulum has swung and it is often applied poorly.
That said, there are other problems in organizations which are prone to, "poorly understood principles, dogmatically applied"...