Check out theman's site.
http://www.protegefaq.net/ Off the top of my head: Intermittent fan speeds 2 and 3, rust around the wheel wells, cracked plastic intake just before the throttle body, rattle in the suspension, some consume oil, cruise control inop and butterfly screws getting sucked into the engine. HVAC issue was fixed at the end of the production run; there is a how to if you have that issue. Cracked intake is common, I would just get an aftermarket replacement. If there is suspension rattle some people have had luck with putting an 1/2" washer under the nut for the strut; doesn't seem like everyone has this issue, there is a thread here about it. Oil consumption: most likely valve stem seals, one person found their oil drains on their piston skirts clogged, one person had it leak from the oil pressure sender only when the engine was running. Oil consumption seems very dependent on maintenance and mileage. Cruise control is sometimes inop for a tail light out of all things! Butterfly screws are supposed only be an issue on the earlier Protege/P5s but I would definitely check the tsb (posted on theman's site) to see if the car you are looking at falls in the affect vin range.
Here's my personal experience:
Flickering fan switch: Started a few months after we got the car. I like to solder so I will fix it myself when I get some down time.
Rust: None
I got a super clean one owner inland Texas car
Cracked intake: I bought a used injen cai from a member here. I would recommend spending $50 on an ebay kit rather than getting a $50 oem part that will crack again
Suspension rattle: Car needs struts so I need to change those before trying the washers
Oil Consumption: Mine consumes some. I have noticed some oil around the knock sensor but haven't wanted to spend the $100+ on a replacement. Also, my car has over 186k mi so a little oil consumption doesn't bother me. The car runs great (although gas mileage could be better.)
Cruise inop: Cruise not working was one of the few issues the car had when I bought it. I now have a tail light issue so it may be the cause.
Butterfly screws: Mine will get my MSP manifold as a hand me down just in case. All you can do is check the vin vs the tsb or pull the intake manifold to see if you have screws or rivets.
I would have a quick read through tsb's and see if there is anything else you need to look for. We love our P5 it is a great car and to us the issues are fairly minor.
