I bought SFO-FRA Z fare for $2200 with LH codeshare on UA. The UA price was over $5000 at that time, but the LH codeshare on the exact same flight was $2200. Of course, I bought it. The two problems with the codeshare are 1) seat assignments are a little strange because you can't see the seatmap properly on the 747, and 2) you don't feel as 'secure' with the LH code share on UA.

If the price is the same, just stick with the operating carrier.