Focus Attack was a serious pain for Ike to deal with even back in Smash 4, but with the changes to landing lag, it should be much less dangerous to work around. You described your friend as "spamming" Focus Attack, but that suggests he was just using it at random all the time, when more likely he was doing it in certain circumstances that you were frequently falling for. To get around it, you have to identify when they like to go for it, and mix up your game plan in those scenarios.
Most commonly, someone will probably go for Focus Attack when you're going in for a Nair or when they're coming in from above you, hoping to tank your single-hit move and counter. In the first scenario, they're probably waiting for you to jump and approach them, so you can throw them off by staying grounded more, tomahawk grabbing like you mentioned, tomahawking only to jump again and punish their focus release, landing out of their reach without attacking and forcing them to make a move instead, anything to disrupt their flow and make yourself less predictable. If they're coming above you with a Focus Attack, fast falling after Nair's early high hit or Uair's huge swing will burn their armored state without putting yourself at too much risk, which then forces them into sidestepping then trying to either evade you or land on your head with Nair or Fair, which you can respond to as you normally would.
On the subject of using Aether to catch an aerial Focus Attack, it can work, but I wouldn't recommend it. You get pretty little reward for doing it, and since it's Ryu/Ken you're dealing with, you're opening yourself to MASSIVE punishes if you miss or they just pop out of it like Aether likes to sometimes do if the opponent's caught in an odd position.