I agree with it being a better episode for those reasons. The way that the Xindii blew the airlock door off, had better energy weapons and that strange 'egg on the wall' thing that exploded darts, the tool that opened the brig door, and the vortex that the two ships disappeared into: they all made them seem much more technically superior and therefor a more difficult foe.
But I was surprised that Archer fell for that old trick of 'planting a spy by having them rescued' ruse anyway. I thought that he was far too naive, and gave her much too freedom around the ship.
It left a few unanswered questions like what Rajiin actually did with her hands, how she recorded the scans, and why she was so interested in T'pol. The Xindii council seemed to have some interanl divisions too. The reptilian species appears to be much more aggressive than the others.
A couple of things were odd. Hoshi said that she'd like to hear Rajiin's language. So, what language was she speaking, English? And Rajiin already seemed to know all about Vulcans, asking T'pol how she could stand to live on a ship full of humans, and commenting on her neurology. Bear it in mind that she didn't say the same things to Dr Phlox.