Aurora not only have half the hp of other tanks, but also tends to miss a lot and cant shoot much upwards-downwards. And needs scauting or radar to use its range. And huge amount of micro. Depends of the map, but on big open landmap, I think most players are unable to use Auroras effectively. New players even less.
Aeon also has worst t1 frigat and quite useless aa boat. T1 mobile aa on land has slightly more health and dps than tanks (not to mention t2...), but Shard (t1 aa boat), is so far from the same comparison with frigats.
Not so much of a problem, but Aeon t1 arty is the only one that can shoot only in front side. So you cant run around and shoot as easily as with other nations. Can be a problem for kiteing, to follow Auroras...
So getting over the beginning, t1 stage, of the game when playing with aeon can be quite difficult. I think this is what most people dont like. Aeon has best destroyer, useless t3 gunship, bad t2 fighter, no fighter bomber, etc. Those are factional differencis, you can compensate with other units. But t1 is hard to avoid.
I dont really see why people would not like to play against Aeon. Might be, that if someone actually chooses Aeon, it might mean that he knows what he is doing and has very good micro.?