Alternate Ability groups

[PK]

Originally Posted by CeeDub

Would you then buy only the two most expensive abilities of each group (A and D) and apply the AA modifier to the rest

This.

For each group of AAs, you pay full price for the most expensive ability and then 1/5 cost for each additional ability. Since your two AA groups (ABC and DEF) aren't related in any way, you treat them completely separately.

Note that there are more complex rules for AAs detailed in GURPS Power-Ups 8: Limitations, in which you can do things like "I have six abilities and I can use any two of them at once." (Basically, you pay full price for the most expensive X abilities, where X is how many you can use at once.)