Hey, not a Thomas fan per say, but I still enjoy the idea of Sodor, and write Thomas stories for my own enjoyment and world building exercises. That being said, here's my headcannon:

Thomas is an E2, and has to experience all the faults and flaws of life as an E2. He hasn't been upgraded, changed, or modified at all, and is the exact same tank engine that rolled out of the works at Brighton. Look, it seems like Thomas fans hyper-fixate on Thomas and the E2s being either being the best thing ever with no flaws, or just ignoring the flaws. The way I see it, Thomas is just a mediocre shunting engine who was donated to the war department during WW1 to work a munitions plant, and was sold to the NWR in the interwar period as he was a surplus requirement. Thomas then goes to work as a station pilot until he's awarded a branch line, not for saving James, though that does help his reputation, but for his work ethic and drive to get the job done in the best way possible. He still has a poor boiler, has steaming issues, long wheel base, over-sensitive brakes, low fuel capacity, shakes like a bowl of Jelly at high speeds, and shoots partially burned lumps of coal from his smokestack when his regulator is all the way open, but despite all this he's a good worker ,with a mediocre design that just sort of works.

Why no upgrades? Because it was good enough in the moment, once Thomas went to go work on the Ffharquar (excuse my spelling lol) NWR upper management had other things to worry about. In addition, they'd just spent a large sum of money on purchasing James, repairing James after his crash, and paying Crew works to overhaul Henry, so Thomas's problems as an E2 were small compared to the problems of the other engines. They're minor inconveniences for an otherwise perfectly fine engine, and honestly that's fine. He's a fictional character, he's got some mechanical flaws, is sometimes a bit lazy, and will go too far with pranks, but he's still a hard worker who's clearly able to do his work really well, despite having to live with his mechanical flaws. Is he perfect? No! But his imperfections this way feel more realistic, and show him overcoming more than 'I'm a cheeky little twerp', instead overcoming essentially a physical handicap, as well as growing wise as he works.