I've owned a Honda and Mitsu and never had any problems. To be honest the condition of the used car you're buying will probably have a bigger impact on reliability. I'm a bit biased with my Japanese cars so I won't give my negative rant about VWs.
Owned a 02 Civic Si and I enjoyed it. The Canadian Si is the American Ex and Canadian SiR is American Si. SiR is manual only. The hp difference between the Si and lower models is quite small so I wouldn't just look at Si. It's a bit slow but it's fun and makes you feel faster than you're actually are.
My Mitsu was an 08 and it's quite different from your 03-06s. Never ran into problems but I felt the Honda was better built.
Not sure what your price range is but I'm a big fan of the Subaru Legacy from the mid 2000's (the sedan not the wagon). I drive a Toyota now and they're reliable
