TLDR version:
So I see a lot of talk about Thunder’s grenade, everyone is trying to compare him to Fragger, but it’s just stupid. I agree that grenades need a little work too, but it’s not his main problem…
But if you want to rework his ability, the best solution is to remove the flash effect and replace it with an electric explosion that deals moderate damage, like 30-50 dmg. It would still stun them, mess with the screen like it does now, but no flash just a bit damage and Thunder would be already much more useful.
Also he is big and slow and his damage output is avarge at best.
So I think what Thunder needs a little buff to his MK46, let’s say increase the damage to body by 1 or 2, that increases the dps of the gun to be a bit above avarge and maybe give him a bit more health so he is not that easy to kill.
Explanation:
His biggest problem really is just being too avarge at everything, he doesn’t have any strong attribute in his kit.
A lot of other mercs have abilties that deal heavy damage, deny areas, etc. even engineers. Also engineers already have the ability to repair/plant/defuse really fast compared to other mercs. So they are already good at least 2 things.
Fire supports deal huge damage with their abilties and provide ammo for their teammates, they’re already good at 2 things.
While we have Thunder who is supposed to be an assault but he is just not that good at it. Even Fletcher is at least as good for an assault as Thunder… Thunder only has a crowd control abiltiy which isn’t that bad, but it only gives utility, no damage like other assaults, and it requires high level of teamplay to actually be effective. But ususally in games your teammates never follow your nades, they just like to hide and wait for kills to come, etc… 
But let’s compare him to the other 3 assaults.
His movement Health and Movement Speed is between Fragger and Rhino, like his size too.
Fragger 150 HP, 385 MS; Thunder 160 HP 375 MS; Rhino 200 HP, 350 MS; and we have Nader with stats more similar to Fire Supports with 120 HP and 420 MS.
Thunder has 10 more HP than Fragger and 40 less than Rhino. While his MS is 10 less than Fragger and 25 more than Rhino.
I think his HP for his size and movement speed should be a little bit higher, like 165-170. That’s one thing he needs.
The area where Thunder lacks the most in my opinion is damage.
His default primary weapon is MK46 which is most similar to Fragger’s K-121.
According to the wiki they have similar body dps, but playing the game it feels like that K-121 jut deals more damage.
MK46 has 11/22 body/headshot damage per hit, while K-121 has 17/34.
While MK46 has higher rate of figher and higher magazine capacity it still doesn’t feel as good as K-121 at all.
It’s a machine gun with the damage of an SMG just bigger magazine capacity.
Yeah on paper it looks ok, it’s balanced compared to other weapons, but the problem is that the only damage source of Thunder is his weapons. And he can run and jump around like a mad goat like other mercs beacuse he is big and slow.
He is like Rhino, big, slow but he has less HP and less damage output.
Minigun has like the same damage per hit as MK46, it’s 10/20 vs 11/22.
Just MK46 has 725 RPM of fire rate and minigun has 1800 RPM.
133 body dps vs 300 body dps and Rhino has shotgun if he gets in trouble, which is also really strong weapon.
As you see Rhino has brutal fire power and high health in compensation for his big size and slowness while Thunder only has avarge at best fire power and an OK crowd control ability that can affect himself.
