Exo-waves are tricky because they often require different tactics then normal waves. While with normal waves you get less warning you know where and the composition of the enemy fleet. With exo-waves you know generally when they'll hit far in advance, but you don't know much more then that.
I will say exo-waves are harder. But once you get into the grove of beating them normal waves are easy.
The first thing to beating exo-waves is to remember that they occur a lot less frequently. As a result, you can fight them and take heavy causalities and still be OK. It can be disheartening losing whole fleets to them, but you gotta do what you gotta do. As long as you don't lose anything permanent or lose more then 4 or 5 planets you can pull ahead between the waves.
Secondly, you need mixed fleets to beat exo-waves because they are using mixed fleets of their own. Defenses alone, even forts, are powerless to the mixed group. You got to fight the waves using your defenses and fleets to compliment each other. That doesn't mean that always fight side by side, but if for example you hold your fleets back until your defenses engage the wave, then flank the exo wave with your own fleet, you would have more success.
It is key to micro your fleets a bit for the waves. I hate micro with a passion but even I micro exo-waves a little bit. For example, the incoming golems should receive the full attention of your bombers, while your fighters engage the enemy bombers.
The best defense for exo-waves is a rolling, or layered, defense. Since you don't exactly where the wave will hit, you can't park your fleet expecting to hit them right at the start. There is a delay. and for late games you simply can't get enough units in the right place sometimes. If you intentionally don't fight hard for the first world hit, but fight hard the world after, you can buy enough time to let your own major fleet meet up and fight back.
Lastly, plan your own offensives around the exo-waves. If for example you see two of them at 90%, hold off on angering that MK IV world until after the wave is broken and you can regroup.