Poor Acceleration and MPG after preventative maintenance

Last summer I was trying to stay ahead of maintenance at 105,000 miles on my 2011 Prius. I changed spark plugs, cleaned out EGR cooler, and replaced the coolant. No drop in coolant levels since then. Soon thereafter average MPG dropped to about 40. I had NGK spark plugs from autozone, and read here that could be a problem. So I swapped with DENSO 3499 {#9091901275, SC16HR11} from rockauto. Only got a mild improvement to about 42-43 MPG when historically it was 47 or 48. Later I replaced 12v battery, added an oil catch can, cleaned the intake manifold, throttle body, and MAF sensor with no improvement.

Finally I took it to a Toyota dealer who said he had to adjust the fuel trims and it didn't have the ISC learning value set. So unplugging the battery for spark plug work cleared some settings I guess. He also said one rear caliper was sticking so I fixed that myself (fully aware of the rear brake caliper position to prevent issues). When I disconnected the battery for brakes it seems to have lost the ISC again as it idled for way too long coasting and stopped. I found this fiddly procedure to reset ISC learning value from another forum which seemed to work.

Mostly the car feels back to normal. I can get up to 46 -47 but only if its fairly flat highway driving. In the city or up hills the instantaneous MPG tanks to about 20 or 25 even with very gentle acceleration. Just feels like the engine is struggling and MPG's drop to about 45. Seeing folks on here claim to get 50+ MPG has me worried / envious.

There are some hints that the drive battery is losing capacity, like some large swings from high to low charge on any given trip. Despite that, my gut feeling is that its somehow related to me messing about with the engine given it happened right after these "repairs". No check engine light and I don't have a code reader. Now I'm at about 113,000 miles. This forum has been a huge help so far but I can't think of anything more at this point.

What else can I do here? Is this just the car getting old?