When comparing MySQL Workbench vs SchemaSpy, the Slant community recommends MySQL Workbench for most people. In the question“What are the best database design programs?” MySQL Workbench is ranked 3rd while SchemaSpy is ranked 7th. The most important reason people chose MySQL Workbench is:
Actions can be directly carried out on tables. The software prepares the relevant query for approval before execution.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Easy to use
Actions can be directly carried out on tables. The software prepares the relevant query for approval before execution.
Pro Community version
There is a community edition available that is free and open source; licensed under GPL.
Pro EER diagramming
MySQL Workbench has enhanced entity–relationship modeling support.
Pro Cross-platform
Works on Windows, Linux, OS X.
Pro Database synchronization
Forward & reverse engeneering

Pro Entity Relationship Digramming for nearly any JDBC-compliant database
SchemaSpy can analyze database metadata in order to reverse engineer ER (Entity Relationship) diagrams for any JDBC-compliant database which includes Oracle, MySQL, Sql-Server and Postgres among others.

Pro Has a GUI option available
SchemaSpy is a CLI tool. For people who prefer GUI-based tools there's one available from a different maintainer which stands on top of the CLI version.
Cons
Con Mixed experience
Doesn't support HiDPi mode on Windows, everything looks blurry. On Linux it has missing features. On Mac seems to be working just fine. But overall a mixed experience.
Con Unintuitive UI
Workbench's user interface is regarded by a lot of users as unintuitive and hard to use.
It seems cluttered and hard to get used to. The left side of the application has several sections (which you get to choose which to open) with several tools for each. A lot of features are hidden behind menus and need some getting used to find them.
Con Freezes constantly
Running any kind of query with more than a thousand records or even just opening a file and other actions crashes the application. You are unable to actually stop a query. You have to kill from Windows Task Manager every single time.

Con Does not work with schema dumpfiles
SchemaSpy has no methods for dealing with when you only have a schema generated via something like (mysqldump --no-data [options] >schema-only_dump.sql
) , and do not currently have access to a live database to connect with.

Con GUI option is a separate download by a different maintainer
Since the GUI version is from a different maintainer, it may be abandoned and eventually break if SchemaSpy development continues beyond that. Or it may implement new features much later than the CLI version.

Con Project may be dead or dying
The codebase on sourceforge hasn't seen an update since 2010.
