I would start by changing out the center to one that matches your bookshelfs, then I would get a better sub.... Polk around the forum a little there is tons of info here, but heres some for free..
#1- front sound stage should be matching set, fronts, and center from the same brand and series, this will give you matching timbre...
#2- Towers in a home theater aren't needed in most systems, towers are made large for their lower end response, but as a trade off you also get some extra cabinet res {not a good thing}, and larger cost... Since in home theaters your avr {receiver} crosses the frequencies so the fronts do not get freqs under say 80hz instead sending them to the subwoofer there is no reason for the larger cabinets...
#3 the most important part of an HT system is the subwoofer, don't skimp in this area...