Generally speaking, with towers, one gets greater volume possible, and deeper bass. However, if we are talking about a home theater where there will be a subwoofer for the deep bass anyway, then there is no need for the other speakers to go very deep. Also, towers in the same model line cost more than bookshelf speakers. This means that if one has a particular budget, if one buys bookshelf speakers, one can spend that extra money on a better subwoofer and get deeper bass. Or, one can spend that extra money on a higher line of bookshelf speaker, and get the upper frequencies better.
With that in mind, what do you want most: Maximum volume, deepest bass, or highest quality of midbass and up? If you want maximum volume, you want the towers, if you want deepest bass, you want bookshelf speakers with the extra money going into a better subwoofer, and if you want the midbass and up better, you want to buy bookshelf speakers in a higher line than what you would get with tower speakers at the same price.
Keep in mind, these are generalities, and some bookshelf speakers of some brands play very loud indeed, so you will want to think carefully about what you value most.
I personally use high quality bookshelf speakers for all channels in my surround system (other than the subwoofers, of course), and my system is capable of playing louder than I ever want to hear it. But some people like to listen to their system at volumes that do permanent damage to their hearing, and so it might be that some people would not be satisfied with my maximum volume.