What should be preferred? A guzetted ex-cadre post via FPSC or specialized department / autonomous body's officer posts. I heard that 2nd one have better salary and medical facilities.

well bro, i am not an authority neither an opinion, but i do back your statement, that autonomous/independent bodies may ensure better career as compared to gazetted/non-gazetted FPSC posts, still, exceptions are always there. Many officers have reached BPS-21 in ex-cadre (IB, BOI, ISI etc) and they all started their career with BPS-17, similarly, there are officers who reached only BPS-19/20.
Also in independent bodies one can get to BPS-21/22 easily (compared to FPSC), depending on organization structure. e.g in NAB, PSO, SBP, Strategic organizations you can go upto BPS-22 (only if heads are promoted from lower formation) otherwise BPS-21 (as in ex-cadre).
ALL in ALL, you need timely promotions to get to highest achievable grade. I would rate SBP (fastest, performance based promotions within 3-5 years) above all obviously after CSS/PMS.

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May ALLAH guide us to the right path :)