The Aegis emulator is not really coded in a very efficient way, you need a really really strong server just to get it to run at all.
It runs through everything in a 20ms interval and often simply can't manage to handle everything in that time, so it starts queueing it and this causes the strange unresponsiveness.
On *Athena emulators we changed this to a 100ms interval (and often even slower for certain things), so it needs 5+ times less CPU power. Unfortunately that also makes implementation of certain things like firewall behavior impossible to replicate to 100%.
