This is my recent experience as well that partner awards price out with the higher fuel, even if your long haul segments are on American Airlines metal. This wasn't always the case. When partner awards were first introduced I booked multiple partner awards staying on American Airlines metal on the long haul segment and was only charged the AA fuel/taxes. This was a couple years ago, however.

Keep in mind though that partner awards are anytime awards. A business class partner award to Europe is 14,000 points and includes intra-Europe flights that may be needed. An Anytime award is 18,000 points and would need to be on American metal only. No one in their right mind would redeem an Anytime award if the you could capture the lower fuel on a partner award as it's less miles. You just need to make the decision if the point savings and regional flights are worth the approximately $1,000 extra cash co-pay (or for an extra 2,000 points and $1,000 you can be in first class on a partner award versus an Anytime business award).