Don’t check-in online, but be sure to be at the airport when the check-in counters open.
Politely and kindly ask the person at the counter if there are better seats available (emergency isles etc.). Usually (from where I’m from, Philippines), the person will genuinely try to give you those seats.
- Write to Emirates Twitter or Facebook Support asking if you can get better seats. I usually ask for seats more towards the front of the aircraft. Sometimes they can give you bulkhead seats before check-in.
Emirates can be a great airline (passenger experience, punctuality, planes, attendants, IFE, premium class product etc.) yet also stink at customer service/follow-up.
Sadly, I’ve found Emirates customer service/escalation/complaints process to be totally laughable on several occassions, which seems incongruent given how excellent the rest of their service is.