Some interesting ideas I've had or seen around for Kassadin are:
Ultimate
1 Have him store up charges. He is capped at say 3-5 charges and they accumulate over time. He still has the assassin, hop in, kill someone, hop away potential. But it is limited to once per fight instead of once every few seconds.
2 Raise the cool down on his ult (I personally don't like this idea because it forces him to retreat by walking which makes him a lot harder to use in team fights. People like Ahri, LB, Zed, Kha can all hop in then hop out after their work is done.
3 As per Kha, make his ult on a high cool down but have the cooldown refreshed or reducded on a kill or assist. This has the potential to make pentakill Kassadin a bigger problem because one assist can send him spiraling out of control.
4 Raise the cool down of his ult, but halve it if it damages a champion. This way he can jump in and jump back out, but the escapes through the jungle or the rift walk up mid until your ult is stacked high enough to 1 shot someone is no longer doable. It would also reduce his roaming potential.
5 Have his ultimate use stacks, but have the stacks gained through the same mechanic on his slow, where spells have to be cast around him. This opens up team synergy and counter play. If Kassadin jumps in and we all use skills on him, he gets a new charge. If we let the ADC/bruiser take him down, he has no mobility. Likewise, a teammate could spam skills to give Kass charges to make his great escape.
Other Skills
1 Reduce the silence duration - it's what makes him the god of mid/assassination. You can't fight back and you can't escape.
2 Reduce/remove his slow - he has two strong CC abilities and nearly unlimited mobility. You can't escape him. If I could at least try to walk away if he jumped in, I would have a better chance.
3 Reduce his AP ratios - I don't like this idea that much because he is supposed to be that one wombo combo type of champion. It may be better to scale some power away from mid game though so he doesn't turn into a god at level 6.
4 Reduce the cast range on his silence. He basically jumps on top of you post 6, so that wouldn't make a big difference in him, but it would hamper his early game harass quite a bit. This would provide more opportunity to beat him down in lane. It would also enable you to get closer to CC him without the fear of the silence in teamfights.
5 Add synergy based on a combo (like brand or leblanc) Right now Kassadin is actually fairly easy post 6. You just keyboard smash starting with R and ending with R. Really bad Kassadins get shut down early, but can often even make a comeback after sniping a few kills. Leblanc has a lot of the same power as Kass, but has a much higher skill cap. Therefore she is rarely banned at lower levels especially.
Make Kassadin have to chose a form of CC for example.
- Q marks someone with a debuff and if he damages them with another spell afterwards they are silenced.
- His slow (E?) marks someone with a debuff and if he damages them with another spell, they are slowed. (Since it's AoE, he would mark multiple targets and could AoE slow them with his ult or target slow someone using Q)
- His ult marks them with a debuff that will refresh the cool down of his ult if he damages them with another spell (So he could spam ult in a fight using his other skills to refresh the CD, but would have no CC)
It would force a Kassadin to chose how he wants to use his combo. If he wants to get the slow off, he can't initiate with Q. If he wants the AoE slow, he has to initiate with the E, therefore exposing himself. He would still be able to do crazy tons of damage, but it would significantly raise the skill cap and make people actually have to learn how to play him properly.
Just thoughts, some of them are original, some I have seen elsewhere but don't remembe who to give credit to (so sorry in advance if I "stole" anyone's idea)