I think maybe to address some of your specifics rather than a general answer may help you better.
Generally, Squier & MIM pickups are not as good as even the most basic upgrade ones. In the past I have waited until someone is upgrading a Am Std or a Am Pro's pups, and I buy them cheap. Still is a good recommendation for you. If you like the sound of the QP's then you are set there, but you mentioned 2 basses so the other can potentially still benefit from an upgrade.
I have found the fret work on Squiers generally in the bad to ok range. MIM's are better but in both cases this is where they save money to sell the instrument cheaper. a hand file and some patience can significantly improve playability. Unless your style demands a very nonstandard setup, I have found MIM's are set up above average for their price point out of the box. Squiers, not so much. In a comparable price range, instruments from Rondo, Ibanez, & Schecter have been much better out of the box than any Squier (and most MIM, to be fair) I've encountered, including the VM & CV models.
I do like to upgrade tuners to Hipshot Ultralites on pretty much all my basses. Many also have Hipshot Kickass bridges, though I look out for BAII's for sale cheap also. I haven't found the nut in any of these to be problematic necessarily, but if you are going to restring and change tuners may as well put a Tusq on it (or whatever else you prefer).
Some things matter more from one player to another. I much prefer a J neck (or even thinner like Peavey or Ibanez) over a P neck, but a good P neck is much nicer to play than a bad J is. Rosewood is going to become a luxury upgrade pretty soon if it hasn't already; if you prefer the feel or tone of a rosewood fingerboard then that alone can mean a potentially large price difference.
When it's all said and done, it makes more sense to me to put money into the style bass you like, than the name; a good MIM J (or player or whatever the new name is) well set up, is a big improvement over a Squier J, and the improvement from MIM to Am Std isn't necessarily worth the price difference. Plus to me, nearly everyone makes a better Fender than Fender does nowadays. This saves people money to put more into an amp & cab, which make a much bigger difference in sound than MIM to Am Std would. Keep in mind my experience is a little skewed being lefty, but I buy relatively many instruments since I can't just go somewhere and play everything on the wall; they rarely have as many as 1 lefty bass in most stores around me.