Since your emphasis is on HT (not so much music), I'd go with atmos. The people In know who have it think it is a very significant improvement!
HT obsolescence is really up to you! My thinking is get a good current system. Any additional screen resolution is like reducing distortion from 0.01 to 0.005 - it measures better but you are not going to experience the difference! A current $5000 HT is still going to be nice 10 years from now and whether or not you upgrade it in 5-10 years and if so, which components you upgrade is entirely up to you. Once gear starts dying, that will often recommend moving to the next generation of technology.
If you are planning to live there a long time, you want to do the renovations right! The important thing is to have a place where you and your family can unwind/relax/do a brain dump from the day (as I think of it). For that you can get away with your 50" and a good stereo as it may make sense to put money into the refurb of the home today and build your HT showroom when you are no longer making decisions on how to renovate. If I was in your shoes, that would appeal to me, because I would actually enjoy the process of detailing out the HT more, once the decisions about the renovation are out of the way.
In the context of home renovation, $5000 really isn't much.
The important thing is to communicate well with your wife and present the HT as a family thing (especially if you have/plan kids). When I was young, Disney presented a movie every Sunday and I bet half of america's families got together to watch them every Sunday night! Propose something like that; the idea of a family tradition/gathering which might even extend part way into teenage years will help sell it to the wife! And if you defer building the real HT until later, make sure she knows you are doing it for the family and home so it is not a fresh topic of debate when the time to follow through comes.
If she sees the HT as your excuse to go into isolation and escape into gaming, she will always resist putting money into making it a better place. If that is a point of contention, negotiate/set time limits.
That was a bit of an incoherent ramble!
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Obviously I don't know your details, but food for thought, or flush it, as seems fit to your specifics.