both car has their own pros and cons...
i owned a waja which is my 2nd ride and was modded with mix and match engine parts. spend quite a lot on enhancement; better suspension setup / pu bushing all round / noise insulation material and changed from plastic to metal power windows bracket all round.
on many occasion, used to swap that car with friend's perdana which was modded with 6a12tt(due to stock engine, esp. the gearbox always giving a problem even after atf cooler installed).
for some reason, i still prefer waja for it's agility. handling wise, waja is a lil' ahead in sharp corner.
to me, it's down to individual preference and most of all, driving style!
without modification, older waja with mitsubishi engine win hands down in term of engine / gearbox reliability and maintenance.
else, perdana for long journey comfort and maybe; looks.