What I think njeneb means when he says he increases GI on surfaces has got nothing to do with the GI settings in the render - he means in the Lighting tab, in Enviro Light, adjust the Strength on surfaces higher. It's a trick I've used in certain unusual situations - e.g. to enhance the reflection of the sky colour in snow. In your render, it would make the darker areas a bit brighter.
Also, please re-read the render setting recommendations tab stickied in this Forum. Although it doesn't mention the RTS, it does point out that for enhancing rays, you should increase atmo samples. The general consensus on RTS, which you have basically confirmed, is, turn it on
only in the Render settings (and if GI isn't a major feature in your scene, you can sometimes get away without it); but elsewhere,
don't turn it on unless you have to - in the atmosphere, this is if
the Sun is behind the landscape (which isn't the case in your render - and there's also a hack to avoid this, using metaclouds - see
http://forums.planetside.co.uk/index.php?topic=7369.0); and in the clouds, I think it is only if
the landscape is casting shadows onto clouds, e.g. opposite the sunward side of a mountain.
Hope this helps.
P.S. Why do you have bloom on? As far as I understand, this is intended to smear out very sharp highlights, like the ones from reflections in water. And of course, soft shadows is also going to up your render time.