Yes, the syntax (or lack thereof, whichever you prefer).
Obviously I'm not entitled to tell anyone how to design their databases. I'm just saying there's good reasons why so many DBs stick to a SQL-like syntax, and that is because the alternatives are usually worse (think: familiarity, tooling, scripting, REPL, etc.).
For example, using the MongoDB REPL, which is probably close to what a datalog-REPL would look like, is rather painful.
This may all be a non-issue when a LISP-language is exclusively used on the client-side. That query-style probably just snaps in naturally there (I don't know lisp).
But if the database is supposed to be general purpose, accessed with lesser languages, scripted, quickly fixed by half-drunk humans at 4am in a REPL... then it certainly matters to have a sane intermediate lingo. Otherwise, at the least, every client-platform is going to invent their own.
I think the example of Cassandra is really a good one to study. They went through an interesting learning-process that seems very applicable here.
Edit: Please see my other comment above. It seems I have misunderstood the project goals and this is in fact not meant to become a general purpose DB. Under that premise my concerns obviously don't apply...
Datomic is, as far as I'm aware, a general purpose database. What it isn't designed to be is a familiar database.
SQL is what people are familiar with, and even some NoSQL databases have distinctly SQL-inspired query languages (e.g. SimpleDB). The problem is that SQL is a godawful query language, and if we want to do better we need to do something different, and therefore unfamiliar.
SQL tries to look like natural language, which has resulted in a syntax is complex, inconsistent and monolithic, just like the language it tries to imitate. If we want a syntax that is simple, consistent and modular we need to throw away the idea that a query needs to read like English.
What exactly do you see as the problem with this example? Or with SQL for that matter?
Honestly, I'm interested in what your criticism is. Is it the syntax?