Personally, I have never heard a stock factory or stock premium system, from any luxery auto maker, that was equal to a high quality, well installed after market system. Of course prices for standard and premium factory systems are generally far less expensive as well.
More then likely, the speakers are just inexpensive paper cones. I find the current speakers, including the tweeters in our 03 RX300 to be quite unimpressive IMO. And as for a subwoofer, didn't really notice that there is one there.
However, for a factory system, the Pioneer in the RX sounds good. It's defnitely far superior to the factory one in the Toyota that our Lexus replaced.
Replacing your stock speakers should yield another noticable improvement in sound quality.
As for the specific speaker choices, Alpine probable makes good speakers, but I have never been an enthusiast of their speakers. I do love their head units and amps though. I have an Explorer with an Alpine headunit, Alpine CD changer, Alpine MRV 4 channel amp powering Boston Accoustic Pro components, MB Quart coax's, and two Rockford Fosgate subs driven by a Fosgate Amp.