The difference to some extent is with lifespan.
An Eneloop has a lower nominal capacity, but it is a very robust cell. You can charge it fast or charge it slow with almost any charger, and it will keep performing.
The higher capacity 2700 mAh cells seem to do better when tested from new, but they are more fragile. After a few cycles you may find them discharging within just a few weeks rather than months. They may suffer more from using a cheaper charger rather than a quality charger like the C9000. An occasional mishap may ruin them.
So your choice comes down to this: if you want the absolute maximum capacity, but are prepared to pay a little more to get it and accept that you may have to replace your batteries with new ones more frequently, then the 2700's may be for you. However, if you want the best long term value, convenience and durability out of your batteries, and are prepared to sacrifice a bit of capacity for that, then Eneloops would be the ones to get.