And for Warhammer Invasion, it would have been the perfect time to change.
It is the only LCG of the 3 that was designed from the beginning as an LCG. AGOT and CoC were both CCGs with existing card sets. I think AGOT players would agree that AGOT cards in the LCG were a bit inconsistent in their design direction, with cards that affect like 1 other card in the set at the time of release. So even with 3x of each card, deck building would still be extremely flawed due to the above fundamental problem. This bigger problem overshadows the smaller problem of lacking 3x each cards and lack of complimentry sets.
Warhammer had the advantage of focus, where deck building would have be possible. It would have been great if 3x are in the core set. Or, at least have the cards released separately for faction building.