I think you need to profile the application like Mike said. Just to be 
thorough, I'd suggest you time the Query execution and the ORM population.

Do you have an example of the faster raw SQL that you're trying to generate 
?

When you do a query on the commandline it is often faster because the 
database is only displaying the initial data on the screen.  When you're 
using something like SqlAlchemy, the app needs to get all the data and then 
create objects.  This is usually lightweight, but if you have some columns 
with a lot of data, there will be a hit.  When you profile, you'll have a 
better idea if the query, the loader, of the connection is to blame.

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