There's two important changes that I can think of that could have messed MyISAM performance:
One is that tasks, milestones, events and weblinks now use another table to associate them to workspaces. Previously this association was done with a column containing the workspace's id. Now it's a table that associates object id to workspace id. It's the same table that was previously being used for Notes, Documents, Email and Companies, so if you have been using
The other is that when filtering workspaces previously we were giving all of the workspace IDs directly in the query and now we are giving a subquery instead of the IDs. It turned out to be much faster in InnoDB when there are lots of workspaces, because otherwise to obtain the IDs you would have to iterate through all workspaces in PHP.
About MyISAM being faster, I thought that too before, but lately I have been searching the web and found several websites with benchmarks showing that InnoDB is faster. On several tests I performed on OpenGoo, InnoDB turned out to be faster, except on some queries like SELECT count(*) FROM table on which MyISAM was faster.