Here is my understanding and thoughts on the issues:
Resonance:
A 3/4" thick panel that is 1' long has much less audible resonance than a 3' long panel. Thus, to prevent resonance issues a floorstander needs to be constructed to a higher standard to attain the same level of cabinet rigidity as a bookshelf.
A quality brand will certainly do this, but the price goes up quickly.
Efficiency:
Floorstanders usually use multiple mid/bass drivers which increases the efficiency of the speakers.
Imaging:
Because the drivers are usually in a tighter array, bookshelfs are likely to image a bit better than towers. But I'm not sure this is a hard and fast rule.
For example, look at Aperion's 6 series bookshelf and floorstanding speakers:
Aperion Intimus 6B @ $250 ea.
Frequency Response (+/- 3dB) 48-20,000 Hz -- (+/- 6dB) 42-22,000 Hz
Impedance 8 Ohms
Sensitivity 82 dB
Recommended Power 50 - 200 Watts
Tweeter 1" Audiophile-grade Silk-Dome Tweeter
Woofer 6.5" Woven-Fiberglass Composite Woofer
Driver Configuration 2-Way
Enclosure Type 1" HDF, Ported
Dimensions 15" H x 8.3" W x 12.8" D
Weight 26 lbs
Aperion Intimus 6T @ $695 ea.
Frequency Response (+/- 3dB) 36-20,000 Hz -- (+/- 6dB) 28-22,000 Hz
Impedance 6 Ohms
Sensitivity 91 dB
Recommended Power 50 - 300 watts
Tweeter 1" Audiophile-grade Silk-Dome Tweeter
Woofer 2 6.5" Woven-Fiberglass Composite Woofers
Driver Configuration 2-Way
Enclosure Type 1" HDF, Ported
Dimensions 41.5" H x 7.75" W x 15.5" D (Base 10.5"x18.25")
Weight 70 lbs
Aperion has a reputation for a high build quality and we see that the tower costs 2.8 times as much as the bookshelf.
The drivers are the same, but the tower has two woofers while the bookshelf has only one. The difference in efficiency is pretty amazing, I don't think a 9 dB difference is typical.
Also, despite being more efficient, the towers can handle more power.
We also see that the tower offers usable bass to 28Hz, while the bookshelfs are at 42Hz.
I believe these trends are typical when comparing towers to bookshelfs.
So, to draw some conclusions, I will toss out the following:
If you really like to crank it hard in a large room, you can over-tax bookshelf speakers; however, a good bookshelf will go pretty darn loud. Ask a showroom to show you how loud bookshelfs will go (let them run the risk) and take note of the size of the room they fill.
Bookshelfs pretty much require a sub if you want decent bass. Towers will give you decent bass when you are listening to music, but maybe not enough for hip-hop or if you are a bass head.
For movies, you'll want a sub to experience the "umph"!
Unfortunately, subs are pretty expensive (often about the same price as the difference in cost between a pair of towers vs. a pair of bookshelves). I think this holds for the Aperion 6's which are nice speakers. $900 is a reasonable budget for a sub to go with either the 6B or 6T.
I believe that typically, the sub with bookshelfs will ultimately give you better sound quality than towers for the same price. However, depending on your room, dedication, and luck; it may take some effort to take full advantage of the sub's benefit. I have a friend (with towers) who turns off his sub to listen to music and back on for movies because he feels the sub hurts the music. I've talked with him about placement, but he simply doesn't want to mess with it.
So, I hope this gives you some ideas on the direction you might want to go.