I know the quick solution is build on every planet and slowly annihilate him. But the issue is that that's not quick and probably wouldn't fly in a me vs. human game.
That will work fine. If you've reached the point at which the AI is constantly running away from you, then in multiplayer a human opponent will likely surrender. We don't like drawing out the inevitable for hours on end like the AI, and the experienced players know when they're beat (though sometimes you can expect a last-ditch offensive, which can be surprisingly effective). The ideal fleet for this kind of late-game play is lots and lots of bombers. Because bombers can cross a gravity well very quickly, the enemy has very little time to run away before you start killing units.
In any case, if you're trying to put on the finishing blow, the key is to hit him in the wallet. At every turn just try to incur expenses for him. Blast his stuff, force him to replace it, just keep up the pressure. Even if he captures a planet, just blast it, and he'll probably end up losing money overall. Eventually you'll bankrupt him and he simply won't have the money to do anything anymore. Another option with planets is to purchase additional hit points, lengthing the time he must spend bombarding them. This lets you catch up to his fleet more easily. If he's using unescourted siege frigates, you can use scouts against them. Scouts are much faster than siege frigates, and a pack of 20 or so (which is actually really cheap this late in the game) will kill them almost instantly if they can catch them. Having a few scout packs on the prowl is not only great for locating where his fleet is, but also picking off weaker unit types, including colony frigates.
It's also possible you may be playing on a map that's too large for the number of empires. Generally speaking, if there are more than 20 planets per player, that's probably too big and you're going to spend a lot of time just covering ground towards the end of the game.
Also is the whole "enemy runs away like little girl" thing fixed in the expansions?
Honestly, this is a "people should know when they're conquered" moment. If they stood their ground and fought back they'd probably kill half a dozen units tops. The AI really should be surrendering at this point.