There are several things to consider when making this choice:
Floorstanders are naturally a much larger speaker, and ideally benefit from a larger room. If you have a dedicated room for your Hi FI or are not pushed for space, floorstanders are a potential option.
If you are limited for space, then a bookshelf may be a better solution. They will give you more room for setup, and may actually offer a more pleasant sound. The last thing you want is a floorstander jammed into a corner, which has no room for set up as you will never get you the sound you are after.
Floorstanders tend to be seen as the preferred choice when it comes to loudspeakers (when nothing else is an issue, such as size, finish etc..) This can be seen from manufacturers such as Tannoy, Advance Paris, Cabasse, Spendor etc.. all of whom offer floorstanders as their reference speakers. That isn't to say that a bookshelf or standmount speaker is a bad choice, and many manufacturers do offer very high end bookshelf options such as Diapason, Rega etc..
Both options will add their own unique sound. Floorstanders can offer a much lower controlled bass, due to the fact they can incorporate a dedicated bass driver and ports. Another key reason is the cabinet size, if you used a bass driver from a floorstander in a bookshelf you would still not get the same amount of bass. Speakers are a mixture of many elements brought together to work with each other, and therefore are designed to work with a mixture of components to achieve the ideal sound.
A book shelf speaker would tend to be much faster, adding a lot of detail and tend to be very precise so its always best to look at the type of sound you are trying to achieve before deciding which option is best for you.
This is where the the bookshelf option really begins to shine. On average an equivalent bookshelf speaker tends to be around 50% cheaper than the comparable floorstander, while also using the same internal cabling. The cost difference will tend to lie with the cabinet size, added drivers etc...So again its worth having a look at the bookshelf option, as it may actually suit your listening needs better, and save you a lot of money in the process. The other option of course is using the money you have saved to invest in cables, which might actually be a better overall sound for you than you would have been able to achieve with the floorstanders.
Both options have there pro's and con's. It may be worth having a listen to a few options, hear the differences for yourself and then looking at some of the variables mentioned above. As always we are on hand for advice, questions or any other help you need .