Since you will have subs, the tower's value is not so great. A good sub will take care of the bass that the tower would otherwise add. Some people like the sound of towers (with subs) better than bookshelves and some don't. Often it is the design of the tower. However, there is no question that two $500 Ultra bookshelves plus $1500 to spend on subs will far surpass two $1000 Ultra Towers plus $500 to spend on subs!
Pogre had the Ultras across the front and after he got a windfall, he bought towers, so he may be able to comment more on the differences. But, really, it is a no brainer for your budget. The real objective is a clean and clear speakers (which the Ultra bookshelf speakers will deliver) and good solid subwoofers which won't detract from your speakers (and $1500 for the pair is about the minimum of where you want to be for that).
I also, because of another thread, just found out that PSA has a pair of XV15se's for sale in their Outlet store for $700 each. He may drop another $50 off if you buy a pair. That is a great deal on a couple of solid vented subs. Here is Josh Ricci's review of the XV15 which is the model previous to the XV15se. They are virtually the same sub, but the XV15se has a slightly better driver, IIRC!
http://www.audioholics.com/subwoofer-reviews/xv-15-subwoofer