I've never played the game. The reviews up on the site don't offer much reasoning for why they give it such a low rating, just saying that it sucks.
Is it a bad game in it's own right for whatever reason, or does it just suffer from comparison to the better games in the series?

From what I've heard-read, it's both. Not only did it take away what made the first two games great (most notably, the many eras, substituting them with only three or so), it's quite bad as it is (for example, the pathfinding is so bad it's annoying to mange even smaller forces).

I bought EE3 and the fact it was on the clearance shelf after a few months should have been a clue.
I don't remember the final straw, that made me junk it after about an hour. I do remember the graphics seemed poor, the pathing was bad, the interface was overly simplified to the point of being awkward. And normally I find these games a bit overwhelming, but to me EE3 seemed dumbed down.

Any idea if there'd be a way to correct some of the issues through mods?

Pretty much Everything.

The units have ridiculous responses when you click on them, the tech tree is dumbed down to the point of hardly existing, units have the worst pathing ever, units are overly large, as if it was intended to be Empire Earth for Pre-Schoolers.

The worst part of EE3 was that once you hit the epoch necessary for air units the game was over. You simply were unstoppable, hands down.

Overall the game was far too easy, and terribly simplified. I'd rather play EE1 than 3 any day, and that is saying something.

Empire earth 1 is more competition. For EE multiplayer visit save-ee.com :D:D great lobby.