First, do your homework before you begin an Extinction Level Event. Establish an embassy so you know what cities he has, and try to identify where they all are. If possible do a map exchange just before you begin.
Second, plan ahead to minimize the time it will take to wipe them out and the chances they have for slipping a settler outside the net. A settler must be supported by a city, so they can only create a new city before you wipe out their last current one. Take a look at the techs they have to see what ships they might be using, and keep scouts around the periphery to see if any laden transports are getting away.
Thirdly, as a last resort, consider tech-gifting them to Worshipful and exchanging maps, followed by back-stabbing. This will wreck your Reputation, but that may not be an issue for you.
Fourthly (probably should have been First), are you playing Conquest games with Restarts On? It's a good way to prolong the game, but often leads to what you complain about. When they restart they get a gift of techs but not a strong enough empire to resist easy destruction. Turn Restarts Off if all you want to do is conquer.
BTW, welcome to CFC! GOTM 38 was a Bloodlust game, and GOTM 39 has Restarts Off too...
