The car does have N/A potential. I would suggest removing excess weight from the drivetrain. Light weight wheels (Sub 11 pounds), lightweight lugs, lightweight crank pulley, and 7 pound flywheel... That unstraps along the order of 30 pounds off of the crank, and that makes a HUGE difference in the feeling of the car.
Next, intake and exhaust need to be dealt with. Header back, take your pick. Intake is up to you, but my suggestion would be to go with a new design of intake manifold. I have a set of ITB's just sitting around, waiting for an ECU. The stock manifold design is 'okay' at best, I'm convinced. Most anything would be an improvement, but really, these changes need to be done in conjunction with an ECU.
Cams need to come at the same time, and you'll want to get a spare head. Work over the exhaust side first and foremost; A lot of material can be removed from there, and should be... The angles therein are a little hairy, too, so those can be smoothed out as well. The cams I went with ended up being in the 270I/280E range, or so, with a touch more lift than stock.
I think the Protege seems slow because a lot of people take a rather conventional approach with tuning it. What I've found thus far, is that the car is just WASTING power, rather than not having it. That, and lots of people strap on oversized/heavy wheels.
