Better in that you don't usaully have to mess with crossovers to split your signal to sub amps or set frequency ranges. Usually with sub pre-outs the HU has a built in crossover and a separate level control. From the deck straight into your sub amps. Less fuss.
head units with sub preouts have built in crossovers to split up frequencies for just the subs and just the mids/tweeters.. in case your amplifiers don't offer filters. these units also give you the choice of up to 6 channels of amplification without the need for an external active crossover. better option in my opinion.