Lucas spelled it out so blatantly.
Qui-Gon's funeral, Yoda says "Always two there are, a Master and an Apprentice" and it cut to a medium close up of Palpatine.
It couldn't have been more obvious if there was a freeze frame with the flashing words "HE'S THE EMPEROR!"
Same thing goes (off topic) for the 6th Sense - it was so plainly obvious that Bruce Willis was dead from the get-go, but I digress....