One big difference is that Aggressors is hex-based and FogEmp is territory based. (That may not sound like a big difference, but it is. For example, you can affect the map a lot more directly in Aggro. You can research road upgrades in FoGEmp; you can send out crews to go build roads in Aggro.) The FoGEmp map is probably larger, too. But Aggro can generate a random map.
Another big difference is that FogEmp has the option of exporting battles to turn-based FoG2 play (even though different studios worked on the games). So if you liked FoG and its related games, this gives your minature-battles A LOT of strategic context.
Aggro is much more of a Civ-ish game than FoGEmp, with all that implies. (At least your units can stack in FoGEmp! -- not always true in Civ-ish games.)
FoGEmp is more like a purely turn-based Imperator: Rome, but it doesn't look as good, but it can have tactical battles via FoG2. I somewhat expect Imperator to out-game FoGEmp over time, though right now they're roughly equivalent at the strategic level, maybe with an advantage to Imperator in most gameplay details.