Pros
Incredibly supportive - doctor's appointments can be arranged easily (which for Japan is not always easy). My supervisor called to check on my regularly, and when I was having a difficult time was genuinely interested in helping me get back on my feet. Professional development is taken seriously and the company tried its best to keep me comfortable. Pay and reimbursements are on time - each position is different, but I had 12 full months of pay, no deductions at all for summer, winter, or spring holidays, plus a small annual bonus. Great proprietary materials, and a management who care about teaching English, not about simply scoring big contracts. 10 weeks fully paid holiday a year and an honest, supportive company - I could not have asked for more. Oh, and they leased me a car to get to work for cheap!
Cons
Nothing that isn't typical of the industry (e.g. at any ALT company salary will not go up, promotions are few and far between, time off during the school year is nearly impossible).