I agree, the upgrade to Blockly 12 was very smooth, but my application is left with lots of these warnings:
Blockly.Workspace.getVariableById was deprecated in v12 and will be deleted in v13. Use Blockly.Workspace.getVariableMap().getVariableById instead.
Particularly noticeable is when my application's unit tests run, as I see dozens of these warnings, which makes it hard to separate out real errors.
Looking forward to a fix landing soon. I'll follow
this issue.