The train infrastructure is not perfect, the biggest issue being travels not going to/from Paris: the lines aren't as good and there aren't a lot of high-speed lines.
Traveling by train through Paris is a PITA as it often involves a station transfer via bus.
It's possible that these options already existed in 2006 but were complicated or inconvenient enough that no one or no web site suggested them to you.
I have and idea of what could have happened though: maybe you took a cheaper train which doesn't arrives or leaves in Paris itself, but in a train station in suburbs (Marne la vallée, Massy Palaiseau and Roissy Charles de Gaulle).
For the train I take to go back home, the price varies between 35€ and 220€. This is excessive! And not much better than sold-out seats..