IMHO, Virtex II is more powerful end cost effective, then Stratix because of many features, which your can't see at first glance, directly comparing number of LUTs, memories, multipliers, and costs:
- distributed memory of Virtex II makes it possible to built very effective FIR filters (based on the distributed arithmetic), large shift registers, banks of small memories and so on;
- Virtex II block memory size is more appropriate for signal processing (especially for multiple channels), then three block sizes of Stratix (in fact, your can effectively use only one of them);
- besides, Virtex II PRO beats Stratix in terms of silicon recourses.
The only very unpleasant feature in Virtex II (not in Virtex II PRO) for me was a dramatic decrease for speed of embedded multipliers in last Virtex II data sheet some times ago - about 1,5 times! (some my plans were distracted).
But nevertheless, when I regularly choose between Xilinx and Altera products for my projects (for more then 8 years), Xilinx turns out to be the best.