You posed an interesting question and I'm sure there will be a variety of opinions. Personally, I don't favor letting someone else 'design my system' because it lets them decide what I should be able to view or be unable to view. As an example, I doubt many (any) currently available 'box' systems offer VCR tape players these days, but I have many tapes and friends stop in with old tapes to share. I do not like combination units such as a VCR/DVD players because if one part quits, both players need to be replaced.
On the other hand, for simplicity it makes excellent sense to stay with a single brand name. As an example, my Phillips DVD player quit and I went shopping for a Blu-Ray replacement deck: I ended up buying a Sony and I was pleasently surprised to discover the remote control unit for the new player also controls my Sony Bravia HDTV. It is a similar control unit and it did not have to be programmed to work with its cousin.
If you are planning to buy a complete home theater system, the first thing you have to decide on the size of the HDTV and bigger is not always better. Ask yourself if you would want to sit in the front row of a movie theater with a 120 foot wide screen in your face or if you would prefer to sit somewhere in the middle or toward the back of the theater. Sony (for one) has an interactive test on their website to help potential buyers determine the proper size of an HDTV based on the viewing distance and not the size of your room. Also keep in mind many old TV Shows and movies do not have the video quality of SD, let alone HD, Their images quite often look much better when seen on a comparatively small CRT television.
A 'box' system will have enough inputs and outputs for all the devices that come included, but will it have additional inputs and outputs to accommodate devices you might want to add in the future? Be sure the system isn't limited as so many 'do-all' 1970s AM-FM Tuner/8-Track Player/Turntables were ... without any way provided to plug in a new Compact Cassette Tape Deck.
A great theater experience also depends on the quality of the audio.
I stole the photo shown above from an ad currently running on Craigslist and you can buy this brand new "750 watt" Home Theater audio system right now, for $50.00 (cash only) and its probably sold from the back of a pickup truck.
With any system, you get what you pay for. If you have much deeper pockets, perhaps something like the systems shown below are more to your taste.