Another part of the problem is that many online travel sites and even the airline sites themselves don't properly allow the entry of partner FF numbers.

I just went through this with a bunch of reservations.

Orbitz is fully aware of partnerships and alliances when buying a ticket - you can search by Star Alliance, SkyTeam or oneworld when buying a ticket. But they have no way to put in a partner FF#, such as using my United MP# on an itinerary with US Airways flights. Tricks such as putting in the whole # with the airline code first (e.g. UA123456878012) doesn't actually get it in the record.

Same problem with Travelocity and Expedia, added by their not recognizing alliances at all.

Delta.com has no way to enter partner FF#s when buying a ticket, so I always have to call their poor outsourced call center to enter my Northwest number.

Northwest actually is excellent in this regard - at nwa.com you can put in FF#s from most of the SkyTeam airlines including DL.

American is like Delta - no way to enter partner numbers without calling in.

Also sometimes the airline systems seem to have problems with partner numbers if you were logged into their website with your own id on the selling airline. For example, if you are logged into delta.com with your skymiles number, it gets into your itinerary. When you call them to add a different number, sometimes it doesn't replace the Delta number.

In general, it's a time-consuming mess. I don't think it's really deliberate, just poor system design, poor integration of systems, and a "our-airline-centric" view of system and data requirements. The FF programs are 25 years old now, but the big airline alliances are only 6 or 10 years old. These things probably just weren't thought out when their systems were built. Airlines that have closer one-on-one relationships such as NW/KL/CO may have built deeper integration.

Personally I'd like to see that it be a requirement of the alliances that their websites take all the FF#s of their partner airlines. But it looks like they don't really care.

I do know that I have booked away from Delta because it's so hard to get my NW FF# in it.