Pros
Health insurance, very stable if you want a job that pays you and does not demand much from you, you are exposed to and learn a lot about various industries (good for networking purposes) you can use Japanese at the work place JETRO is good mainly as a temporary job / launching pad for a better paid job. Only work here if you need something temporary or are in a midst of a transition.
Cons
No opportunities for raises or promotion as a local staff. Management rotates every two to three years, so there is a lot of instability in terms of consistency and continuity in projects. Lots of overtime Paid below-market wages as a local staff 401 k plan is not good (recommend getting your own IRA account instead) As a foreign govt, JETRO does not pay your state and federal taxes, you have to file as "self-employed" even though you are a full-time employee of JETRO. You also cannot deduct any expenses as a "self-employed" taxpayer due to IRS rules with foreign governments. Filing taxes is quite a process because of this, so be prepared for that if you decide to work here! A very traditional and conservative Japanese work environment, might not be good if you are not used to working for a Japanese company/organization