Just to be clear, you're referring to micro ATX mobos right? The heat is due to the components being closer together, not necessarily a design flaw of the platform itself.
Regardless whether or not I'm right about mATX referring to microATX mobos, I would first try to get a detailed picture of my components' running temps before considering adding to your cooling setup. Who knows, your CPU could be actually running at only 50C or even 40C under load?
What are your temps?
are you overclocking?
Which case do you have?
I'm asking this 'cause I don't think any system will get too hot under normal conditions, considering 2x 120mm fans (exhaust) and the PSU taking air out too.