I think the first thing you have to do is to separate the regular AC website from PTO. They are very different products. PTO has some very positive aspects, but a number of shortcomings. The AC site, with a couple of exceptions is execrable. There also some slight differences with the award booking site but I'll include those with the AC general site. Here is my list of pros and cons for both:

AC site:
Pro:
1.Booking class is shown when flights are listed
2."Shop for fares" gives flight combinations for cheapest fares

Sorry, can't think of any more.

Cons:
1.Lack of ability to request by booking class
2.No way to select any routes other than those AC listed ones.
3.No capacity for multi-segment selection
4.Seats are assigned with no ability to request (no seat maps)
5.When trying to select an award flight, the message saying that the flight combination is not available does not say which segment is not available. This means a trial and error hunt for availibilty.
6.Award reservations have to be confirmed by phone (is this still true?)
7.There is no way for Es or SEs to gain access to revenue inventory if W (for E) or D and W (for SE) are taken

PTO:
Pro:
1.Excellent real time seat maps
2.Ability to select any routings and airlines. Can even set preferences.
3.Multi-segment trips (up to 8)
4.Ability to save itineraries
5.Relatively simple interface with full selection of flights
6.Reasonable on finding lowest fares

Con:
1.No way to book (or even see) booking class
2.If you want to look at both J and Y seat maps you need to go through the "find" process again.
3.Inconvenient if you want to play with different itineraries e.g. if you change one flight that results in a < 30 cnx, you can't get the seat maps and have to change the other flights to fit. Same if you want to look at different dates. These restrictions should only be flagged at the point of making the reservations.
4.No access to award bookings with this system
5.System is not hooked in well to AC's regular booking engine (e.g. when trying to construct a > 8 segment R/T by creating two o/w itineraries, these cannot be merged automatically by an agent. They have to type in the second part manually).

I'm sure there are more in each of these sections, but that's all I have for now.

One thing that we should all remember though, is that the needs of the likes of FT members are quite different from the once a year vacation pax. We want maximum control of every aspect of the booking process and have the knowledge to make the best use of all the resources that are available. A person looking for a cheap flight for a summer vacation needs a very user friendly interface that provides information about flight availability and perhaps seat selection, but he or she doesn't care if it's L or V or Q class. It seems to me that AC should have two distinct products, one that caters to the uninitiated (a la Expedia or Travelocity) and one for the frequent traveller. I almost always start the booking process online, but then I'm forced to call to get more information. I'm sure AC could increase its online reservations massively by taking into account the travellers' needs.