Low cost check in is different to full service check in.
Full service - Counters open three hours before departure, and there are more of them. Allows passengers to check in as it suits them without waiting too long.
Low cost - Counters open two hours before departure and there are fewer of them. Passengers lined up waiting, staff working continiously.
Instead of paying three people working "slowly" for 2 1/2 hours, low cost pays two people working quickly for 1 1/2 hours, and gives them a lower hourly rate.
Basically if flying low cost, come early and be prepared to queue.