Generally speaking, stand-alone speakers are always better than TV speakers due to the limitations that TV speakers have. Are there some stand-alone speakers that are just crap? Sure, but I would expect the speakers that Onkyo boxed in to be better. Have you tried any of the calibrations on the receiver? Is the sub working? Also, any other reason you haven't connected the other speakers? Regarding Optical, while you can only do 5.1 and can't get lossless audio with optical, it should still sound better than stereo speakers.
For me, surround sound is important. More so than video, but I know most don't agree. Surround Sound, when done right (i.e. Dolby Atmos) adds so much to both movies and games.