Overall, I absolutely love this car. My only major complaint is that there's occasionally excessive cabin noise from the brakes. I also wish that the gear ratio between first and second was a little closer. Aside from that, I get better than posted mileage (I average 31 mpg mixed, 34 if I'm only driving highway), the seats are extremely comfortable, the handling is close to perfect, the design is original and attractive.
The rally shifter. I'll never want a floor mount shift, ever again. Seats. Responsive steering (it had the most responsive FWD steering I've ever had the pleasure of experiencing) and tight suspension.
Auto-up/auto-down on passanger window, fully retracting sunroof. Larger cupholders. MP3 CD player. Better noise dampening (the road noise isn't awful, just the brake noise). 40 more hp would be nice. Maybe a full size spare, if they can fit one? No major improvements necessary.