Owning an 03 Spec V...I don't have much to say about the 02s.
But Personally I wouldn't own an 02, they have alot of problems compared to the 03s. The tranny, I dunno, It's like REALLY REALLY notchy, I thought the 03 was pretty bad (after test driving RSXs and Celicas) but the 02s are :s
Stock for Stock the MSP out does the Spec in performance. It's not a huge diffrence but it's there.
The Spec Would win for other things like higher crash tests (w/o side impact airbags) CC, sunroof, side impact airbags.
If you plan to mod...I would say it all depends on how much money you're willing to throw into the car. You can make any car handle like a go kart, and be as fast at the strips..it all comes down to the $$$.
Now without doing any major engine/tranny build ups (Ie reinforcing) the Spec will probally edge out in terms of power.
Handling...well concerding both already have good suspension setups already, I believe the protege's chassis is stiffer than the Specs, edge wise...handling...the protege would probally edge out the Spec.
Again both of these are quite marginal.
I personally say (I know this is now off topic) if you really wanna get rid of your spec, find a used 2000 Celica GTS. Hotkics just released their suspension kit for the car...on stock engine...and modified suspension it like went 75.2 mph down the slalom (which is now a record for a sport compact car, apparently) and pulled off 1.04 Gs down the skidpad. Testing was done by SCC. (expensive, but worth it) (the protege and the spec will probally need alot of suspension work, more than the celica needs to do that)
Oh yea, and 1/4 speeds, intake and exhaust on a GTS will drop you to like low 14s easily. (I don't think it's that easy on the protege or the spec)
And the car is a sexy sexy beast.
And the look is nice...but the only problem comes is finding a used celica GTS 6-speed that HASN'T been ragged on.
But I really perfer new cars to used...you never know what's happened to a used car.
Personally if you're planning to mod, and performance is all where it's at for you, I'd stick with the spec, with the slew of JWT developed mods for the engine comming out...you can have like a 350whp Turbo car or a pretty powerful NA car easily.
IF you plan to stay stock (or really close to), and performance is more important to creature comforts, go with the MSP.