I’d disagree with a frame upgrade. If the frame geometry fits and the specs (travel, angles,…) fit your needs not anything you can really upgrade on a frame.
I agree fit is crucial. Which is why it is hard to say whatever bike is the best and at least riding one in a parking lot is key. This is why I changed the crank (to go to a 165 from 170), bars and stem (shorter stem, +20 rise bar) first thing with the Salsa build I mentioned above.
I’ll add brakes if you do any significant downhill. Most off the rack bikes come with sub standard brakes.
Wheel upgrades are hit or miss with MTB. See my argument above that weight dosn’t matter on a MTB. I usually wait until I trash a rim or hub.
For wheels when you need them I’ve done 3 sets of Lightbike. First set I purchased their rims and built my own. Last 2 sets I ordered from them built. They are top notch, I highly recommend them.
Light Bicycle's carbon mountain wheelsets are suitable for XC, AM, EN, DH, Trail, E-bike uses. A wide array of hub, spoke, nipple options available. Customizable 100%.
www.lightbicycle.com
Frame: You're right that you can't really upgrade anything on the frame after you have one that works for you. But for me, there's a significant difference between carbon and aluminum. The last aluminum frame I've owned was a Santa Cruz Nickel. Great fit and geometry for the time but it definitely wasn't stiff enough for my 175lbs. By the time you get an aluminum frame to the same rigidity of a carbon equivalent, it's too heavy for my tastes. The issue with carbon is as
@coleAK mentioned, it's not as durable to outside damage. It's definitely stronger than aluminum, but it won't handle rock strikes like a metal frame. However, I've taken a metal bat to a scraped SC frame I have and it's quite impressive on what it will take. Sharp objects are its kryptonite.
Fit / stem / crank: Changing those parts for fit is crucial to the ride quality / enjoyment. Changing those parts as upgrades, as a lot of people do, is just for bling.
Brakes: These can be a worthy upgrade, but are mostly personal preference. Going from 2 pot to 4 pot may or may not be an upgrade depending on what, where, and how you ride. I prefer Shimano brakes and I love the 4 pot brakes on my squishy bike. But since I ride my single speed differently, the XTR Race brakes are a perfect fit. They don't have the on/off feel of the servo wave and work great for what I do. I do have to question the "upgrade" people do to go from Deore 4 pot to XT 4 pot brakes. I've ridden both, and it's not a performance upgrade.
Wheels: 100% agree with the Light Bicycle stuff. I started riding wide (30mm inner) carbon rims in 2013 with some Nextie's. Oh my, was that a game changer. Watch the PB Friday Fails videos and watch for the endo crashes. You can easily see the front rims flex and spring back, almost making it harder to recover. No scientific data to back that up but watching the research videos is entertaining.
Weight: This one I feel is worthy. It's right up there with "this 6 inch travel bike pedals like a 3 inch travel race bike". No, no it doesn't. It may feel a lot more efficient than 6 inch travel bikes of 5 years ago, but it's not the same. The efficiency that comes from a stiff lightweight bike can't be duplicated any other way. Dropping 2 pounds of wheel weight will drastically change the way a bike rides. And when going on a 4 plus hour ride, a 25 pound bike is less fatiguing than a 30 pound one. If I'm not riding big drops or super chunky trails, I can ride longer and feel better afterwards by taking my singlespeed. That's comparing a 28 pound SC 5010 with Push suspension to a 21.5 pound titanium singlespeed hardtail. I will say that my previous SS was carbon and weighed in at 19.5 pounds. I prefer my Ti one. So there is some flexibility there in when some added weight is acceptable.
This is just my opinion. Not meant to be argumentative or discount other peoples preferences. I just feel that most upgrades people do are personal upgrades that don't actually produce a better bike or ride, it's just something they want.