It depends on what you want the rifle for....
If you want more conventional scope mounting, and accessory options then go with the flat top, I say conventional because contrary to what most will tell you the carry handle really doesn't limit your options you just have to buy a seperate mount, and usualy mount your scope a little higher than normal....
If you want to be "Tacti-Cool" meaning buying every gimmicky accessory or fad as was stated earlier then go with the flat top....
If youra collector and are going for as close to an M-16 as you can legaly get, then get both (By the way the flat top is M-16A4 style, not A3, the A3 is identical to the M-16A2 except with full auto instead of burst...., but personaly I reccomed getting the A2 first, as thats whats in the widest use by the millitary....
If your going for an SHTF rifle than get the A2, if you get the flat top then thats all the more parts you can misplace, the rail can get dirty, or banged up rendering it useless, and the Iron sights of the A2 are much simpler....
If your a plinker than I recommend the A2 as it's sights are generaly simpler to use....
Now as for price you should shop around the prices that shop is charging is to much though it's about right for Bushmasters theres other brands that are much cheaper and just as good I recoomend ADCO
www.adcofirearms.com/rockriver/rraffl.cfm?page=rra the A2 is about $740, and the A4 is like $705 but I don't think the carry handle comes standard you'de have to ask, alternativly you can also get the parts seperately from them and build it yourself, or shop around, however there barrels are all 1:9 and not chrome lined, but you can get the barrels from elswhere if your going for something else ADCO will even install it for you for free if you order one of there rifles (RRA....) and knock a hundred bucks off the price, Bushmaster carrys both 1:9, and 1:7 barrels both chrome lined but you'll have to specifiy 1:7 when you order, or you could look at Fulton Armory, they carry a variety of barrels, includeing chrome lined ones of varieing twists....