I was also in the same quandery however after choosing Good hope Flying Club I feel that I made the right decision.
It takes about 15 mins. to get there from the city centre (without breaking any laws).
There are alot of experienced instructers there, and they are now OK with enough A/C.
P.E. is a dive and not particually safe whereas I haven't seen any problems in cape town in the 8 months I've been here.
Let me know if your coming