I've used my Stilo for a couple of longer trips now
3-dr vs. 5-dr, Argonaught summed it up the best, you buy what you actually need. (I don't need the 5-dr and I prefer the looks of the 3-dr).
But even storing things on the back seat of the 3-dr (like, laptop, briefcase, jacket etc.) becomes a pain after a while; you start to curse the front armrest, and the catch to release the driver's seat backrest feels like it's going to break every time you use it. Incidentally the driver's seat does not move forward when the backrest is released (the passenger's seat does). These are minor points but they highlight what it's like to live with the 3-dr.
One thing that afflicts my Stilo (and I suspect the 5-drs as well!) is that it's VERY easy to lose things under/beside the seats where there's little clearance! A friend lost his mobile phone, I've lost keys (many times), and a torch has become standard glovebox equipment for this reason

The gap between the seat base and backrest (already mentioned) and the cut away sides of the seat base, and also the nice smooth leather, mean that everything from a piece of paper to the laptop computer can just slide right off, ending up under the seat where it tangles with the wires/adjuster handle etc.
You might think this happens to all cars - but no, on small cars like the Uno and the Punto, the seats are a lot higher off the floor (and the rails are on the sides). There's often also a 'wall' (crossmember) under the seats that prevents objects sliding backwards out of the front footwell. Unfortunately the seats themselves are not usually much good
A quick look under the Stilo reveals most of the difference: the floor is higher because there are stiffening 'beams' underneath! The older cars had basically a tin pan which left more room under the seats, but less rigidity...
As for the comfort of the Stilo seats - good, but not great. I have the seat as low as possible, which puts the lumbar support in slightly the wrong place. Better than many small cars, but can't touch my old Alfa Romeo 164 for long-distance comfort. Or the even-older Lancia Thema! Those cars are really in a different class for comfort, though the refinement and safety is probably nowhere near modern standards.
The reason you feel that you're sitting high in the Stilo is due to the size of the car, in my opinion. It's a lot taller than the older cars and the dashboard is vast, while the sides of the roof are wide to accommodate the airbags, giving the impression of having your head in the ceiling.
Personally I liked the reassuring driving position of the Stilo from the outset. I don't want to be rude, but if it doesn't feel 'right' after playing with the seat for a few minutes, then it probably won't ever feel right

It might be worth trying some other modern cars for comparison.
I haven't driven an Alfa Romeo 147, but suggest that it may be a better choice for driving position/comfort? I'm making this suggestion on the basis of the Alfa Romeo market positioning... and the experience of that 164, it was a fantastic drive...

Also, 147s are of similar age/features to the Stilo, so will be a similar price? (they are over here, at least)
Incidentally I read in Top Gear that the FIAT seats are made by Lear Corporation in the USA (not the aircraft...), and I think it's fair to say that they're a lot better than FIAT seats of old.
-Alex