A lot of comments here from T Spirit owners - here's my perspective from the other end: I've traded up from a Renault Megane (53) to a T3...
First of all I'm very happy with the car - coming in at the bottom of the range I probably don't have such high expectations. I can understand how some details become more important for top-of-the range owners who are comparing with more upmarket cars, and no-one likes to see a backwards step from an older model. But for me when it comes to the Gen 2-3 comparison, none of the gripes come close to outweighing the improved performance, driving feel, space and above all economy of the Gen 3.
Key features missed by me & already mentioned:
Outside temperature reading should be up on the main instrument display & as we approach winter a frost warning would have been appreciated - agree with DaveR.
The various option buttons in the centre console look smart but require looking down - agree wholeheartedly with SilverT4 on that one.
I haven't filled up with petrol yet but it sounds like the Megane had a better design: it didn't have a door release lever or a filler cap, just a sprung metal flap that sealed shut on its own (the outer flap locked when the vehicle was locked). However, I notice the Prius has a little arrow on the fuel gauge icon to show which side the flap is - a nice touch since we're going so long between fill-ups we might forget

.
The Megane had auto headlights and auto windscreen wipers as standard and I think the dimmable rear view mirror was standard too. Of those I think the auto headlights were the most useful, but for me front fogs as standard on the Prius trumps all three.
A couple of observations of my own:
The Megane had an engine temp display and showed the oil level when starting off - but maybe Toyotas are so good you never need to worry about that ?

I like to adjust the mirrors help reverse park and can't easily find the control at night as it's not illuminated.
The front windows don't clear condensation/rain when opened & closed.
Although the cabin storage seems a bit more limited the Prius has more cabin space overall, especially in the back, and is only marginally longer (and a little narrower) than the Megane.
A more obvious one to finish with: I expect to carry bikes on the car at some point - the Megane had mounting points on the roof for securing a roof rack, rather than clamping onto the sides, and of course Toyota discourage a rear-mounted carrier/tow bar/lighting board.