Lessons we have learned:
* Television sets don't last forever. Plan ahead for replacing the television set, and don't assume that the replacement will be the exact same dimensions as the one you have now.
* Think about proper ventilation so your electronics don't cook themselves.
* Think about the wiring behind the components. Make it as easy as possible to access the back of your components when you need to get to the wiring. If you have complex wiring, then keep written records or label your cables well. Think about how you will route the wires between components, and leave extra space for the "excess" from longer cables. You can make or buy custom-size cables, too.
* Think about remote wiring in the wall behind the home theater. Now may be your chance to bring in extra electrical circuits or outlets, Ethernet, cable TV, HDMI, speaker wire for remote speakers or multi-channel (surround sound), etc. We have conduit in the wall behind our home theater. The conduit runs up to the attic for whatever wiring we want, a real boon to us.
* Think about speakers and audio carefully. As @woodnthings
pointed out, building the speakers into the cabinet may not yield the best audio quality. (Exception: the center channel should be in the center.) Remember that speakers may need eventual replacement, too.
* Think about how you will move the home theater out of the way when the need arises. Someday you will install new carpet, paint the walls, upgrade the baseboard molding, fix electrical issues, ...