Even simple things can make them a better instrument.
I can tell you what I've done with mine, all Affinities.
The first thing I do is get rid of the cheaper 500k mini pots and tone cap. I follow Fender specs and replace with full size 250k CTS pots, a .047 tone cap, and I upgrade to better gauge/quality wiring then what Squier uses. I believe standard Fenders use 22 gauge, where the stock Affinity stuff is pretty thin. Just doing that can bring new life, even if you retain the stock pickups.
My strat has stainless steel block saddles, similar to the old Fender Strat Pluses and a brass nut that I cut and shaped myself. I plan to replace the tuners with vintage style tuners soon, as the stock ones are 5 years old and getting a bit rough feeling.
For the basses, I have also upgraded the pots,caps, and wiring and shimmed up the necks to get better action. I plan to get better, vintage style bridges with brass saddles, put brass nuts on. Also nicer tuners at some point.
I haven't spent a whole lot, and I do my own work, so it saves labor costs.
You can do a lot with these things for not too much, and if you want to go further, one certainly can.
Whether or not it's worth the cost is up to you. If you want a nicer instrument, right off the bat, and one you should have to do less to, buy an MIM and just upgrade simple things. If you want the satisfaction of playing something you really built up yourself, I'd say gut the Squier and go to town. But you'll never get back what you put into it, if you were to sell it at a later point.