I traded a 2004 MCS in on my 2006 Si.
The MINI is more nimble but the Si - to me - is more manuverable. I know that sounds weird but in autocross I'm turning better times with the Si.
Day-to-day I like the Si a lot better. I like having a trunk again and the seating position is more comfortable - although I had more headroom in the MINI (yes my seat is all the way down.)
Gas mileage wise they're very close but I tend to drive fairly hard. The MCS has a supercharger kick and whine but the Si has the VTEC kick and growl. Plus the Si is 197hp versus 168 hp for the 2005+ MCS. FWIW, my wife complains now that her head slams against the headrest when I accelerate hard - she NEVER said that when I had the MINI.
Oh, and if you think the Civic has a lot of TSBs, check the MINI. It went back for several ECU updates while I had it and never got rid of the yo-yo (do some research - it's all out there about that.) My wife's 05 MCS doesn't yo-yo but I've been in other 05's that do. Mine also went back for an emissions recall and I had to have a new transmission at 3200 miles.
Lastly, I considered the TCO. MINI is owned by BMW - which translates to $$$ whenever it has to go in for service after the warranty expires. And no-one knows how long it will last since it's only been out since 2002 in the USA. Honda has a proven track record of longevity (my 90 CRX is about to turn 200K miles on the original engine and clutch.) Also be aware that MINI dealers can be few and far between depending on where you live and BMW dealers can NOT work on MINIs for warranty due to the franchise restrictions.
Ultimately, drive both and get whichever one you prefer. The only person who has to be happy with the purchase is you.