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I've heard nothing but bad things about ZODB. I question the wisdom of building a database on top of a python database.

I agree and I have worked with ZODB. It isn't a database, it is a mediocre persistence ... thingy. You store objects and now your database is tied to your code.

Have experienced nightmarrish scenarios when updating codebases.

I consider ZODB as more like a framework for quickly building databases. ZODB developers (we've talked to many of them) consider upgrading objects as no-problem (because they have very well understood patterns for that) etc.

While that's ok for Zope/ZODB developers, it's not for an average user. We need to wrap it up to make easily usable, without requiring developers to read tons of documentation and "Design patterns" in advance!

And, obviously, some universal json query language is needed

How are you going to manage querying ad-hoc fields? AFAIK every field within your ZODB-query needs to be indexed in ZODB first?

Indexes are created where you told them to. So, if you include an arbitrary field, it's probably not going to be indexed to start with. And yes, query is for indexed fields.

I guess, we can have another type of behavior where all new fields are indexed. It doesn't sound like a "clean way" to me, however some developers could desire that

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