Wonder Woman always was a powerhouse character. The problem was, that after Crisis, they tried to turn her into Superman, and it didn't work. While Perez was on the book, the sales were good, and they've gone up and down, depending on whom was writing and drawing, but with the increased mythological basis, she still didn't really work. One of the other things working against her, is that the costume is directly tied to World War II, and that's been excised from the Earth 2 origin.
The strength of the invisible jet (originally, invisible plane), is that is shows the development of the Amazons. They weren't just kicking back peeling grapes for 3,000 years, they were a vibrant, thriving, and progressive society. Removing that from the book weakens it from the foundation. Many people complain that the jet is silly, but I maintain that it's the un-updated graphic representation that is the problem, and not the basic concept. Especially now, as stealth technology is advancing, it makes more sense than ever that a race that's done nothing but explore the boundries of science for millenia, would be a bit further ahead.
Combining this aspect with her physical strength, agility, and endurance, puts her on equal footing with both Superman and Batman, and I believe, does far more to legitimise her place in DC's Trinity.