Those expansions also did not do that well in the US. The only draw of those sets were the unique Crystal types that were released in the Aquapolis/Skyridge sets, but those lacked the playability that the EX cards have.
I also believe that WotC did not meet the standards that Nintendo had placed on them. When the contract was up for renewal before the release of the Sapphire/Ruby set, WotC offered a lower amount for the contract than Nintendo was willing to settle for, and hence, the property reverted back to them.
Frankly, I have no complaints with Nintendo's handling of the Pokemon TCG. Yes, I receive fewer cards per pack, but, I enjoy the revamped reverse holos and that they're releasing more promotional cards(ie. Pop series) now.