First, you need to decide if you're going with a 5.1, 6.1, or 7.1 system. My personal preference is to go with a 5.1, and putting the money saved from the extra surrounds into the other speakers. But if you're mainly into movies, you might want the extra surround speakers for effects.
Second, you need to consider the WAF. Is the room dedicated to movies? Is it a designated man-cave? If so, you might get away with some sizable boxes. If the room does double duty, or the wife doesn't like the look of large boxes, you might need to go small. Do you have kids or pets? If so, towers or floorstands might not be as good a choice as wall mounts. Personally, I don't like them, but the ultimate wife/kid/pet friendly speakers are in-wall mounted.
Third, you need to consider your budget. You don't want to spend all your money on speakers, and not have enough left over for decent electronics (however, your speakers are the most important component of your system, and will probably be the largest expenditure). There are a lot of choices available, and you can put together a better system than a HTIB, but it doesn't do any good to look at Wilson speakers if your budget is $2000 (it doesn't do any good to look at Wilson speakers even if your budget is $20,000). Anyway, if you've got a pile of money, its easy to put together a great sounding system. Putting one together on a realistic budget isn't as easy, but it can be done.
Going with separate components (not in the amp - pre-amp - DAC - etc. type of separates, but separate as in individual speaker / sub-woofer / electronics / source) is that you can use what you have, buy a better component now, and upgrade the rest later as your budget allows. Look for sales - close outs can do wonders for your budget, or allow you to step up in quality without blowing the budget.
You said you're having a house built - you're having this room pre-wired for sound, I suspect? Its a lot easier to run wires through walls during construction, and the results look a lot neater. You might want to go ahead and wire it for 7.1 (or even 7.2) sound now - you don't have to use the extra connections, but you'll be glad you have them if you ever do.