My vote goes to Permanent Waves.
The other two albums do IMO not suffer (or hardly) from negative aspects such as these:
Even though I am getting more used to the happy, over the top "let's have FUN"-hallalujah mood of the opening track, I prefer music of a different vibe.
And hearing it as the constant (or at least very often?) setlist opener is coming a bit out of my nose (sorry, Dutch expression). Besides, live, Geddy doesn't sound that nice on it. I really like Peart's drum patterns on it though.
Also not a big fan of Entre Nous (this was the song Billy Corgan talked about). Not very enthralling melodies and I feel that the jumpy, happy music in the couplets and choruses are out of place, when comparing it with the more concerned theme of the lyrics. The instrumental parts are more dramatic though, but not very captivating.
Natural Science. Fantastic beginning, build-up and couplets and then it all gets worse when they start jamming some totally irrelevant and unfitting music.