I think the major change from ISE 4.2 to ISE 5 is it's place and route engine. The place and route engine is now much more powerfull than before. I Implemented a big 6 million gates design with both of ISE 4 and 5. In ISE 4, I could gain better clock frequencies when I set some additional area constraints. ( Some area constraints in addition to what you set for your modules. ) However in ISE 5 I could never obtain better clock frequencies using this technique.
This means that the place and route engine is doing it's work very very well.
Additionally , There is now a new tool PACE in ise 5, which lets you to do the pin assignment process much more efficiently. Using floorplanner you have difficulties doing pin assignment, specially when using I/O signalings other than normal LVTTL, such as SSTL or ...
The area constraints can now have shapes other than a simple rectangle.
I think there is much much more, and It is really a good idea to switch to new ISE.