If this is going to be a dedicated home theater space, I would personally go with a projector. That being said I have seen many installs done various ways based on the need of the customer. A few options to look at.
-TV and Projector, I've seen some solutions go this route as the TV is used when you do not want to have the room at darker light levels or do not want to burn through the projector bulbs. This is accomplished via higher end receiver units which have 2 hdmi outputs. Receivers such as the Denon 3113CI have two video zones which allow for not only using a tv and projector in one zone but outputting different video and audio to two zones.
-As far as speakers go, I prefer Bowers and Wilkins. The own the market in speakers which cost over $1,000 a piece. While expensive, they simply are they best. Martin Logan also makes a very high quality speaker, the electrostats are phenomenal and have a very deep and wide sound stage. I would stay away from anything in wall as the quality is lacking compared to a floor standing or even bookshelf. Keep in mind that a true bookshelf speaker will port to the front vs the rear, an important note to make when choosing speaker location.
-HDMI Cables, while there are some people that will say "the cheap cables will do" this is not the case. Its very complex and with 4k coming there is a lot of data needed for 7.1 or greater audio along with a true 1080p signal. A great article on hdmi cables is located here: http://www.monoprice.com/home/home.asp?pn=help&idx=12
-Controlling the system is another hurdle, you can go with something very simple yet limited such as a Logitech Harmony system to a URC system which will be programmed based on your individual system by a system programmer or even something like Crestron or AMX. If you are looking at something like Creston you may want to look at Control4 as it is an easier system to use and it is modular to expand into other areas of your home such as lighting/climate/security.
I've been out of the HT game for just under a year now but I was a Magnolia employee for four years and have done a lot of custom installs for customers.
My suggestion is to head to a Magnolia branded design center and they will set you up with something really nice, it will be expensive though as the word "discount" doesn't exist in their world.
Check out Magnolia at http://magnoliaav.com/
, they offer a service called consultation (not sure of the current price or promotions) but its well worth it as an adviser will walk you through your needs and design a custom solution based on what you want done with the space.