You are talking about your main living room. Both of you view it as the focal point of the house, where you will spend most of your time, and where you will entertain friends and relatives. She probably has a significantly different concept of what that room should look like than you do. When you say you will "integrate" the system with the room, you probably mean you will set up the system where you think it will sound/look best, and position everything else around it. I can almost guarantee that is not her concept. My suggestions would be:
1. Ask her about how she would like to see the room, and really listen. After she has fully explained what she wants, you will have a better feel for how to "integrate" your ideas with hers. Somtimes spouses just need to be listened to, and if you do listen first, you can then explain your point of view and maybe negotiate an acceptable compromise (see recommendation 3).
2. As others have said, either two channel or HT but not both, unless you do as I have and integrate the two using one of the many available preamps with HT pass through so you can use the front speakers for HT also. Look at BAT, Muse, McCormack, Adcom and others for the pass through option.
3. Think of ways to "hide" the electronics, most women don't want to see them in their main living room. Unless you are talking about a dedicated listening room or HT room, the less seen the better she will probably like it. There are some nice furniture quality entertainment centers, or you could look into some other approach to "camouflage" the offending equipment. I have an antique european wardrobe, that I have gutted, reinforced and constructed equipment shelves inside of. The only equipment that can be seen are my front speakers and my BAT vk-500 amp that has its own stand. Everything else, including the television is in the wardrobe.
Let us know what you try, and how it works. Good luck.-Tim