The bottom line problem with third-party opaque vendors is that everything is just fine until it is not. If one can save EUR 5, why not? On the other hand, when things go wrong, the ability to have them fixed by the plating or operating carrier (depending on when the issue arises) is critical. When you purchase through one of the vendors, check:

1. Reputation. Not from friends and colleagues who may have had successful trips, but where there were problems during the trip which were properly handled by the vendor.
2. 24-hour customer service. It does you little good to be standing at NRT only to find that your vendor does not open for 5 more hours because it is located in Europe and is not open.
3. Fees. Bear in mind that vendors may impose their own fees above those imposed by a carrier and they may impose other conditions such as inflexibility above and beyond what the carrier imposes.
4. Ticketing. Sometimes it is possible for a vendor to issue an itinerary through the use of multiple tickets. That is fine so long as one understands that one is not connecting but simply transferring between tickets. Transfers are generally not protected, meaning that if you no show for your onwards flight, your ticket is cancelled and you must purchase a new one and are responsible for your various ground expenses.
5. Quality of customer service. How long does it take to reach someone who is in a position of authority to fix a problem. Again, standing at NRT only to be told that someone will call back within 24 hours, is not customer service.

While there is always the possibility that a vendor can replicate "full service" at deep discounts, that is rarely the case. The cheapest ticket is not always the least expensive journey and the failure to do due diligence on someone where you are spending significant sums online is your responsibility.