IMO, most bikes under $1k come with pretty generic cheap wheels. Upgrade what you have. I have not used them, but Vuelta wheels get good reviews and can be had reasonably cheaply at Nashbar and other spots. Bicycle Wheel Warehouse has lots of options too.

I wouldn't get hung up on 50% of new bike price. It is all about how much money leaves your pocket. If you spend 70% of new bike price and upgrade to parts you love, you have parts you love and 30% of new bike value in your pocket.

Granted, I spend way too much on upgrading bike parts, and building up my own bikes, but every ride I enjoy all of the pieces that I picked. If you have never tried upgrading, try it and enjoy the process.