A lot of champions that are kept at low winrates either have to be there for the health of the game or are weak just because we are in a meta that doesn't really favor them.
Champs that are kept weak for the health of the game:
Ornn
Kalista
Nunu (getting reworked so doesn't really matter)
Nid
Gragas
Sej
Galio
Azir
Ryze
Shen
When these champs are super strong they completely run over high elo and pro play while still only being able to maintain close to a 50% win ratio in low elo. Ryze has a 47% winrate and has been nerfed over and over again, but is still seeing a ton of pro play just because of how busted his kit is in the right hands. Azir is never allowed to be strong because mid lane then becomes Azir vs people who don't auto lose to him (which is not a lot of champs when he's strong). Those champions will most likely stay weak until they get reworked or have significant changes to their kits. There are other champs that should be on the list, but those are the only ones I can think of off the top of my head.
There are a ton of champs that just aren't good atm because of the current meta were in, but I don't wanna make a huge list of them. If you look at some of the lower winrate champions you can generally tell why they are weak. For example, Kog is pretty weak right now because engage supports are more popular and peel supports are not very prevalent in the meta right now which makes surviving as him much harder.
There are also just some cases where champions can't really be buffed with just number changes. For example, it is harder to buff/nerf Brand based on just numbers alone because if his numbers are too high then he is a busted support and if they are too low, then he is complete ass at everything. It can be too hard to find a middle ground for certain champions without making them overbearing so it's harder to buff them without making them game warping.