To me, it is use and budget that make the difference. At around a couple hudred a pair, you will get a better bookshelf than a tower IMO. Better that the funds difference goes toward a better sub which will yield a more well rounded budget system, vs. towers with no sub or a lesser sub. Cheap towers sacrifice many things to get down to this price range.
Move up the food chain to a few thousand a pair, likely a tower will be far more capable because they're more focused on getting things right and you'll get better cabinets, drivers, x-overs, etc...
Then there's your focus - music or movies. For movies, IMO, towers aren't really needed, particularly in the budget area. If the primary listening is music though, for me, I'd put all of the speaker budget toward the best towers I could get (probably still end up with a sub though).
My system is ~30% gaming, 30% movies/TV, 60% music and I don't have towers.