Modeler is just the name for version 12 of Monarch. The basic idea is still the same - you teach your computer how to read a document - but there are underlying improvements. In version 12, you can now have more fields, more external lookups, more multi-columns - all of these improvements in power are a result of the architecture changing from using local Access as the underlying database to local SQL.
Updated Excel import and export, and improved PDF handling, are also new in v12. Modeler also introduces a change from the old XML formats for models and projects, and replaces these with binary DMOD and DPRJ formats. It can't save back down to the old XMOD and XPRJ formats but it can read them.
I don't think there are any significant missing functions. Weak linking between objects defined in external models is one, but not many sensible people would be be doing that anyway.