My question is, is there a significant difference in the accuracy between "mid level" and fancy AR-15's? Would an off the shelf S&W MP-15 be handicapped under a Stag Arms or Noveske? I understand there's probably a price difference but will a lower level significantly hold me back? And, if so, can they be upgraded to the same (ish) level of accuracy without essentially replacing the whole rifle?
The S&W M&P's that I've seen shot very well. I have a Stag 3G upper and it's good. I'd put the S&W and the Stag as equals for accuracy and I would have no hesitation to get the S&W to get in to the game at a reasonable price point. I'm not sure what the specs are anymore, but they used to come with a Daniel Defense free float rail and that was really a worthwhile option to have.
If you handload for it, you can likely improve it's precision. I should note that I only require 1 MOA accuracy, so once my load reaches that, I do not bother going any further, so the Stag may have more potential than what I report.
Replacing a barrel is easy to do, but is still best to have someone with the correct tools to do it. Headspace should be taken seriously. Triggers are also very easy to install and you can do it with no prior experience and a little care and attention. But anyway, upgrading later is easy to do and your thinking is correct. The rest of the upper assembly is not hugely different from upper to upper.