2000cc VS 1600cc (VTEC 16 makes less power)
In NA form, easier to modify the Honda
Turbo route obviously suits the 3S via conversion
Handling etc is much different, you'll likely have more fun driving the SW20. If comparing to a DC2R, it is faster all round than a SW20 NA.
Take a ride in one & see how you like it I guess. Aesthetically, I think the MR2 looks much better. Horses for courses.