It depends! If you don't mind large speakers in your room and you have the space to place them properly, then choose large speakers. They’ll sound great. If you have a small to moderate size room and you don't have the space to place large speakers properly, then small speakers will sound better. It’s easier in this instance to place small speakers in locations to provide superior imaging and it’s also easier to place a subwoofer for better bass response. You might be pleasantly surprised how good small speakers can sound.
But there are some tradeoffs with tiny speakers. They won't play as loud as large speakers (although plenty loud enough for most people and rooms). Those little satellites cannot reproduce bass of their own, making it tough to achieve a seamless blend between satellite and sub. There is often a hole or weak response in the lower midrange area (bottom range of a male voice) where the satellite’s response leaves off and the subwoofer takes over. When evaluating sub/sat systems listen closely to male voices; if they sound thin, the system suffers from this midrange suck-out problem.
The other issue is bass response. Some of the so-called subwoofers in these systems are passive (not amplified) and should really be called woofers because they don’t reproduce the truly deep bass with authority. If the system is to be used for only music, that may not be a problem. But if the primary use is home theatre, you may later find the need for an additional powered subwoofer. Many sub/sat systems now come with powered woofers that are worthy of the name subwoofer. As always, listen before you buy and trust your ears.