Okey, what I had in mind was, getting caught off guard, or getting attacked by something you cannot defend against.
You have two bios. You got to know all the weaknesses of your bios, and get rid of them.
Take my Luffy bio for example.
His first and biggest weakness was: No sensory ability what so ever. So I had a lot of blind spots. Someone could just pop up behind me and slice my throat.
What'd I do? Well at first I used chakra sensing rain, chakra sensing rain has a lot of weaknesses as well, so one can easily avoid it.
Next I learned sound from Nero, and used the inner sonar skill. But it still wasn't strong enough sensory ability, because it couldn't detect opponents underground, or opponents that are moving really fast. So I upgraded it, created a CJ. Which is one of my most precious custom jutsus. I made sure my technique didn't have any blind spots or weaknesses.
So the foremost and most important thing is to get rid of all your blind spots. Never get caught off guard.
On my Kiyoshi bio, I already had the kiyoshis ability to sense energy, so I didn't have to worry about that there.
Now for the ones you mentioned:
A genjutsu that restricts your movement. Well it might restrict your movement, but it doesn't restrict your chakra circulation. So you can use a burst of chakra to get out of it.
Because you cannot see it, doesn't mean you cannot defend against it. You can feel it right? That's enough. Those are tricky to defend against, when you feel it, it's already harming you, so that means you wouldn't have time to do a jutsu that requires a lot of handseals to defend against it, but if you use a quick jutsu to defend against it, you can continue the battle with minimal damage from it.
MS and EIG have always been tricky to defend against. But luckily the opponent cannot keep spamming it against you. MS exhausts the opponent after 1-2 uses, so if you are able to defend against it, you'll be ahead. EIG only lasts for 3 turns, and it also exhaust the opponent a great deal, depending on how many gates opened. The clue about fighting MS is to stay out of sight. If they see you, your dead

MS is doujutsu, eye technique. If they cannot see you, it's pretty useless (with the exception of susanoo, but you just need to stay away from him, should be easy, don't get too far off the ground, and just use hurricane fist or some other technique that makes it easier for you to dodge its strikes.)
When fighting against EIG, even if you cannot keep track of their movement, doesn't mean you cannot defend against it before it happens.
EIGs weakness is: No ninjutsu above C rank. That's what you gotto take advantage of. Using EIG gives you some pretty strong jutsus, but if they cannot reach you, for example, if you go deep underground and build a fortress under there, you'd be safe. For example, as the opponent is opening his gates, you quickly use hiding like a mole technique, which enables you to dig really fast, and then, go deep underground. Since you are actually displacing the earth around you, you should have some oxygen supply. And when you reach deep enough, you quicly use, Nagashi to destroy the earth around you and use some earth dome or something, for example. To do this properly, you'd need a sensory ability, so you'd know what ur opponent was doing above ground, since a strong punch can create earthquake, so if you have sensory ability, you'll know when to use nagashi.
Just an example.
Got it?