I'm going to keep a running list here of the things I like and don't like. Some items will appear in both categories, because there are aspects of some things which are both good and bad.
Exterior style. I thought it was OK when shopping, but it's really grown on me. I've seen a lot of complaints about the large-mouth-bass look of the front grille, but that's something that hasn't bothered me at all. I think it's less noticeable on the darker colored cars. The 18" wheels look very nice, and I've received some compliments on them already.
Interior Dash Design. The dash layout is definitely minimalist, and I like that a lot.
Interior Comfort. The longest I've been driving at any time is maybe 1.5 hours, but I found the seats and seating position to be reasonably comfortable. I'm a little over 6 feet tall, and when I lower the driver's seat I have plenty of headroom. The backseat legroom and headroom is better than I expected.
Handling. The cornering (at least on the SE) is surprisingly flat, especially for an econobox. I've pushed it fairly hard around corners at speed, but not hard enough to lose traction on the still-new Dunlops. The torque-vector braking effectively eliminates understeer, making turn-in feel surprisingly (almost unnaturally, see 'Dislikes' below) quick when cornering hard.
Manual Transmission. It's simply a lot more fun to drive a car with a MT -- even an econobox.
Engine. It's not the most spirited sounding engine, and it feels a bit reluctant to rev at times. Almost like it has a heavy flywheel. But a big part of that is that the fly-by-wire accelerator is calibrated conservatively such that more pedal travel is required than expected. Once I got used to giving it a bit more pedal, it gets around pretty quickly when needed. Again, having a MT allows finer control over the RPM/available torque, and that helps get the most out of this engine.
MPG. So far, so good. First tank was 36-37 MPG, and second tank looks like it will be 40-41. Mostly rural driving at 25 MPH - 45 MPH.
Noise. I'm not sure whether to blame the Dunlops, the lack of sound-deadening materials, or both. Especially when the tires are cold I hear and feel a subtle bump-bump-bump of the front tires while turning. At 30 MPH the road noise is noticeable, and it borders on annoying at highway speeds. The wind noise isn't severe, but it's definitely noticeable at highway speeds. On a recent ride into the city on some bumpy roads, there was a persistent buzzing rattle somewhere around the driver's side door frame or headliner between the A and B pillars.
Ride Quality. Over perfectly smooth pavement it's really nice. Over typical/decent roads it's acceptable. Over bumpy roads it ranges from OK to fairly jarring. I think in Toyota's zeal to make the SE "sporty enough", they favored aesthetics over practicality with the 18" wheels and 40r/18 tires. I think 17" wheels and a little more rubber would have been a better choice, and sufficient to distinguish it from the non-sporty trims. I have 16" wheels with 205/55r/16 tires for winter driving, and it will be interesting to see how the ride quality improves with these. I'm sure some of the...stiff/harsh ride quality is due to the suspension tuning.
Handling. While I appreciate the torque-vector braking, it takes some getting used to. It seems like it doesn't always come on smoothly/progressively. If you're in the middle of a sweeping turn and then turn a little sharper, the vectoring system seems to kick in kind of abruptly. When this happens, you suddenly go from a predictable, mildly-understeering FWD car, to a "Holy @#%! I'm oversteering!" kind of feeling. If you're not prepared for this it's alarming at the least, and potentially dangerous. I've had a few times where the car was understeering a bit during a high-speed entrance ramp curve, and I was reluctant to turn any sharper for fear that the sudden switch to oversteer would cause me to lose traction. It can sometimes give the perception of a sudden shift in direction that might make you lose control of the vehicle, or even rollover.
Clutch/Shifter. The clutch engagement point is too high. It takes a bit of getting used to, and until you do it's actually easy to stall the car when starting out in 1st. This is exacerbated by the large amount of accelerator travel needed before enough fuel enters the system. The shifter was butter-smooth at first, but now it's sometimes a little hard to get into 1st gear.
Infotainment. Sorry, Entune 3.0 stinks. It looks boring, is laggy, and isn't particularly intuitive. The best I can say is that, for the most part, I've figured out where to go to find relevant information. Toyota promoted Alexa integration and Remote Connect, but neither of those are available as part of the regular Entune 3.0 system. The only thing on the infotainment system that I use is Apple Carplay and the Eco/MPG screen.
Lane Tracing Assist. Again, Toyota marketing fail. Lane Tracing Assist is strangely missing on the 6-speed manual version. It's not a feature I anticipate using, but it bothers me that it's not there.