Sometimes he even runs away SCREAMING, is this the teen stage? Their mom was this way, squeak when picked up. Does neutering help with this? He tend to be pretty cuddly when I hold him in a pouch, tough.
When I first got Meeka she was like that - It took a few days of showing her that all the noise in the world would NOT prevent me from picking her up. Is it a pain sound? Is it only when you touch certain areas? If not, it may be something where you just show him that all of his protests won't stop you from loving on him.
Hmm. It sounds a bit like a temper tantrum then. If it keeps you from picking him up he might keep it up. If it does make you hesitant, maybe start putting a treat into your hand to see about coaxing him to you?
And if it is a temper tantrum, then maybe you can get him more in the mood by giving him a treat after you do pick him up to associate the two together. But there's a danger that he'll associate angry squeaking with ways to get food.
I have three rats. The oldest is perfectly fine being picked up. She's very sweet. The youngest struggles with being picked up at first and will curl her toes when clinging onto your arm (not sure how to describe it but there seems to be a way a rat grabs you when she's uncertain about her surroundings). The middle one actually scurries away if it looks like you're going to try to pick her up. When she is picked up, she whimpers and also curls her toes when clinging.
The funny thing is that even the nervous rats will come up to me all lovingly and kiss my fingers. The middle one often puts her front paws on my hand while safely keeping her haunches in the cage. When they're riled up (usually in the evening), they're perfectly happy jumping up on me and crawling along my arms and shoulders—as long as I stay near the cage so they can hop off when they want. They're very confident when it's on their terms. When I pick those two up without permission, they don't like it (but the youngest is coming around, just not as relaxed as the oldest yet).
Mamma, my skittish rescue, used to get very upset when I tried to pick her up. I started using treats to encourage her to come to the cage door and now that she's got cage door equals treats down, I'm working on making her take it a step further so that she has to climb out onto my hand before she gets the treat. She's doing well with that but likes to take the treat and scurry back into the cage so we've started to use baby food which she adores and it forces her to sit in my hand if she wants to nom.
You could try offering a bit of puree/yogurt/other soft foods on a spoon to him and then while he's eating pet the parts that make him fussy once he's chowing down. Don't get discouraged if he runs off the first time or even the first dozen times. Just keep with it and the results might surprise you!