The built in subs are more a space issue and look issue, than a sound issue. Maybe a WAF issue also....:-)
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Often the prefered placement of the speaker to reproduce low frequencies is not the same as the prefered placement to reproduce a realistic soundstage. This means that more often than not a compromise has to be made unless you have complete freedom of placement.
This being said the sub/sat combo is difficult to integrate well (cancelation, crossover slopes, etc).
Read the stuff about the Vandersteen subwoofers if you want to really understand (or be really confused). I personally like stereo subs and good bookshelf speakers when properly integrated.