I have a 2007 MS3 sport, my fiance has a 2007 Honda Civic Si 4-door; without bias I can tell you somethings, however let me 'tint' them so you understand my perspective:
I am 6'4" 320lbs, size 46 waist, 32 length. I am a Big-Boned individual; have a even layer of padding, but am not 'obese' any longer; this is to clarify 'fat' from just 'big and tall'. That said:
I love my MS3 seats WAY better than my g/f's Si. Her lumbar supports bite into my back and I don't quite fit between them; they must be made for more narrow people. My seats, on the other hand, are fantastic and I fit like a glove -- the lumbars work wonderfully. I HATE her dashboard; I tell her we should plant corn on it to make a buck off the extra real-estate. I don't understand why the dashboard in the Civic is as big as my glovebox; I really like how big my glove box is, btw - and a passenger can get into it while sitting in the seat. Not in hers, it opens right into my knees, and then is TINY as hell. Perhaps the knees thing is 6'4", but not the tiny space in it; the MS3 glove on the other hand can realistically hold a fricking 12 pack. On performance, her gears are very crisp, though I really don't care for the way the shifter is; it reminds me of an Atari joystick. I like her display inside, the 'look' is indeed futuristic or very 'techy' feeling; MS3 is more like a cockpit kind of feel, I think F-14 is to MS3 as Blackbird/F-22 is to Si. MS3 feels more 'tried' and 'analog' where the Si is like the cutting edge, just the way everything is lit and displayed. For drink storage/door spaces MS3 is cool, I can fit a drink in each door, two in the middle, and one in each door and two in the middle in the backseat; Si is two in the middle front, two in the middle back. The door slots in Si are not big enough for more than magazines/PSP/CD players. Acceleration; she has more 'equity' in 1st and 2nd, but like has been said, I'd PWN her every time in her Si with my MS3. I don't like how our first gear is sometimes (under hard pull/WOT) more of a 'hurry and get to 2nd' than a real 'gear', lol. Under normal acceleration it is fine. Headroom is equal in both; I am a bit more comfortable sitting on either side of my car than hers, I think for a shorter person the layout of her car provides perfect 'resting' spots for long drives, such as the door trim molding for your right/left arm depending on where you are seated. Mine is seemingly made for me, the resting places are intuitive. Both cars have awesome armrests; these things are like Texas, gone are the days of shifting/pushing subtly for space with the person beside you like in a movie theater. Her car has better stock sound/stereo, but mine makes cool lights left or right on the deck when I change the volume.

Helpful, I hope.