The MP3 overall has 3 differences that are confirmed to make that additional 10 or so bhp...
2 come from the ecu, 1 comes from the intake manifold. The ecu uses a different ignition table than any other protege ecu, which in most cases translates to 8 or so degrees of advance...something the short rod, high piston acceleration FS engine desperately needs...The other ecu difference is a noticeably leaner open loop afr database...both the normal proteges, and the mazdaspeed proteges, go ridiculously rich at the switch from closed to open loop modes...where as the worst, the msp, can be almost dangerously lean up to around 3700 rpm, then so rich you could almost see raw fuel coming out the back...
the Mp3 ecu has a MUCH better switch from closed to open loop...with it being safe in closed loop for high loads, and a gentle increase in richness as the revs increase...on dyno's you can clearly see the difference...the mp3 has always had a very nice stable torque and power curve, where as the standard car's (and unmodified msp's) curves look like ladders...you'll often read from normal protege owners, when switching to an Mp3 ecu...that the biggest difference they feel is a much smoother power band...and that that the engine responds much better to throttle input than it did before...i can vouch for that, i just switched a month ago...
the 3rd difference is from the lack of a system known as VTCS in the mp3...the ECU doesn't have the control parameters in it, but that is sort of irrelevant...as the intake manifold also doesn't even have the butterflies for the system at all...I don't recall if the MSP has this, but normal proteges definitely do...and even when 'off', the system is very constrictive of intake flow...especially at higher rpm...
some will argue the MP3's axle back exhaust also makes some of that 10hp...i highly doubt that...both the mp3 and normal proteges have a crimped down-pipe that is a complete joke...as well as the two catalysts...those things are by far the biggest restrictions in the exhaust...NOT the muffler at the back...so without adjusting those problems, i can't see how a slightly free'd up muffler will do anything on its own...its generally accepted that the MP3's axle back is simply an aesthetic change...for appearance and sound...nothing more...