The reverb in Reason 2.5 is a bit tastier, but I know what you mean by extra frequencies cropping up - there seems to be a problem with harmonic distortion. Also, there does seems to be a 'thinness' to the sound.
Although when I noticed this, I did an a/b with cubase and reason using the same drum samples in Redrum and Battery... The result sounded identical. I think the problem occurs more when layers are stacked on top of eachother - things get very muddy very quickly, and nothing sounds 'big' enough.
Thing is, now I don't like the sound of Cubase. Logic sounds far better to me!
Try burning each layer out as wav and loading them into Cubase or Logic. Use high bit rates and sample frequencies.
Or re-wiring into either sequencer. Cubase is easier to handle for this.
The Reason EQs are shit - no shelf/high pass filters. (Low pass is manageable with the filter unit. Not ideal though.) How are you expected to properly bracket your sounds?
Getting proper EQing on the sounds from Logic or waves EQs will help loads.
Tequila