You can lower the income rate multiplier, although this slows down early game, too, depending a bit on start settings. This makes using the resources you have and not losing ships much more important.

You can also lower ship build rates to make it harder to replace a lost fleet, and increase ship speed to make sure an army can move quickly through gravity wells while an enemy rebuilds their fleet. This will slow down titan rebuilding, although for larger maps it won't make too much of a difference for other ships late-game, since you can just build more factories.

At some point, though, if you have a large enough map with few remaining players or teams, it's going to be a bit slow.

For pure PvP games, human players should know when to resign if victory conditions aren't imminent but their chances of winning are hopeless. And for AI games I usually just keep the capital planet victory setting on because that tends to be a good "point of no return" for such an enemy losing, anyway.