For media purposes, a trinity has never made sense. DC needs to keep the focus on the Big 4: Superman, Batman & Robin and Wonder Woman.
For fanboy & story purposes, Diana didn't make any sense being on the same level as Supes & Bats. She has a diehard but small fanbase, but has pretty much had one title compared to multiple Batman & Superman family books.
I'd imagine it has more with who Harry considers a threat and that it's not a DC Comics mandate to slight WW.
I hate to comment on this out of context. Maybe it will be a plot point later on that this guy underestimates women. But it certainly seems like the writer/editor at least are downplaying the power level/dangerousness/importance of Wonder Woman in favor of Green Lantern, and that seems like a bad idea.
Well. there's more to this, I don't think Harry is actually all that interested in killing the Superheroes, he's trying to convince Stormwatch to attack them in the hope that they will kill themselves in the attempt, so he picked the most dangerous members, or ones that can exploit Stormwatch's weaknesses. and he may be counting on Diana coming to Superman's defense in the fight against Apollo. (not that the story ever actually gets around to them fighting Superman etc.)
The thing I noticed though is... why is it Hal Jordan on screen? he's "dead" it should be Baz.
I almost wish DC did try to recast their "Trinity" to include GL instead of WW just so we could watch them get raked over the media coals.
Of course, sales-wise, it makes sense because those are the three that support multiple books. But Wonder Woman is the one with the personality to stand up to the others, as seen in JLU and New Frontier.