You pretty much have it. Towers look nice, are typically 3 way, bookshelves are typically 2 way and need a little more care with placement, but you can typically get a better sounding system with bookshelves+sub then towers+sub. I went with towers due to children running around and the wife wasn't sure about stability of speaker+stands, but otherwise I would have gone with bookshelves.
I'm sure it will come up, so here's a post by WmAx with a great suggestion:
"Seriously.... Get 3 pairs of Behringer B2030P 2 way monitors : LINK : ($150 per pair) + 2 of the Dayton 12" powered subwoofers :LINK : ($80 each on sale)
These monitors are vastly superior to any Bose speaker, and I mean this in a provable/objective manner. In fact, this 2 way speaker is superior to any other retail produce anywhere near it's price, to my knowledge, based on provable/objective critieria. The subs offer the best value for the $$ possible. You need two of them for 2 reasons: (1) Louder SPL and lower distortion on music or movie peaks like explosions, etc. (2) Using one on each side of the room allow for far better integration - the 2 way speakers will act like 3 ways with no seem in between for music playback. BTW, you can make the sub sound 'tighter' for music, if so desired, by simply adding in a common cheap $3 polyester filled bed pillow in each cabinet. An easy and reversible cheap modification that will really increase the bass sound quality for music.
All you need now is a decent home theater receiver with a decent built in active crossover. Set all speakers to SMALL and set xover to 80-100Hz and you will be good to do. Since you will have two subs, one on each side of room, 100Hz is a better choice for crossover point selection.
No how, no way, are you going to get anywhere near the performance for the dollars spent buying new equipment if you choose any other 2 way speakers.
If the speakers are too large or ugly, you can substitute them with Infinity Primus P152 2 ways. These may cost a bit more - but are smaller and offer great performance for the $$. They don't have the superb wide dispersion, extension, smooth treble or dynamic range of the Behringer units, but they are smaller and look better. You need to use 100-120Hz crosover point using these speakers if you want to have ability to do considerable dynamics in movies. With the dual subs - 120 Hz is not a problem. Just keep each sub within 3-4 feet near each main Left and Right speaker.
-Chris"
Source. Post #8.