For the Safety Issue...
Protege:
http://www.hwysafety.org/vehicle_ratings/ce/html/99005.htm
GTI/Golf
http://www.hwysafety.org/vehicle_ratings/ce/html/99001.htm
Oh yea...not having a rear-independant suspension isn't THAT big of a deal. if that were the case...then every car should be outhandling the Spec V...but it isn't...since Spec V's can easily keep up with ITRs in Autox and on twisty roads stock for stock.
But from my experience..I wouldn't trust my life to a protege in an accident. A friend of mine was killed in his protege, going about 80KM/h head on, seatbelts, but the frame just collapsed on him and killed him.
A sentra has better crash reports, then with the new added side impact air bags it's even better...another friend took a lamp post at 100KM/h head on, walked out without a scratch, just a minor burn from the airbags deploying (which all 4 of them did).
From my experience the protege is quite a dangerous car to be in.
Also from what I've heard the GTi is like built like a tank heh...
But unless you are planning to crash your car, that shouldn't be of any concern, although accidents do happen.
It all depends, the GTi with a good suspension kit can be made to handle like a dream (but that's the same with any car). GTi can make power quick and easily. And it's internals are very strong. It's also a much more refined car, and has a lot of luxury elements to it. The one thing I HATE is the drive-by-throttle lag, I know it's expected that there should be some...but my spec v has none, and the lag on the GTi isn't bad...but it annoys me.
The MSP is already pretty modded out of the box, it's got a decent sound system, supposedly a super sensitive alarm. It has awsome handling, and it's limited edition. But...you lose out on cruise control, and sunroof. Modding is pretty limited too. The handling seems to be better than most of the aftermarket can produce for the protege...but I'm sure simple things like, stiffer springs can yet improve the handling of the car, I'm pretty sure full coilvers would be even better. Boosting...it's kept mild for a reason...You can't really boost the crap outta the MSP without changing the internals, about after 10 psi, that's what you wanna do if you don't want a blown engine. But it's got more room, and yea...4 doors.
It all depends what you want. If you're looking to mod...the protege isn't the huge place to be since the aftermarket is really small...the GTi's is pretty large, so getting really good parts for the car, that have been tested over and over again are easy.
But if you REALLY wanted to mod hardcore on a FWD platform...you should get a used EG/EK civic...for the price of a MSP/GTi you could mod the hell out of a EG/EK civic (yea a civic...but it's got like the most aftermarket out of any car I know
)
But why are you limiting your self to only these two cars? There are plenty of other good cars out there for the same price. Just look around, decide what you want, do your own personal research, other people's opinions are good...but there is no opinion that isn't biased...you should come up to your own conclusions