After read some issues, there are two major concerns:
1, backward compatibility.
2, implicit commit is bad, tolerates bug-prone codes.

However they are not contradictory if we print a warning when doing an implicit commit. Some messages like this:
    Warning: sqlite3 module issued an implicit commit before executing VACUUM, you should commit this transaction by yourself, that's a good habit, etc..

Then we can keep backward compatibility, and no longer commit implicitly.