Alteration needs something, it's incredibly bland. I'd say give it elemental aura based spells that are location based - a flame circle, a frost circle, a lighting circle - and have enemies take increased damage from an element while you take less from the it. Gives it some synergy with destruction and conjuration(atronachs), and currently magic skills are lacking in synergies compared to combat/stealth. Hell, maybe make the auras charge your ward so it does elemental damage when enemies strike it, so that it also has some synergy with restoration.
I can't speak for conjuration or destruction(a lot of criticisms about it from others)currently, haven't really tried them enough.
Alchemy needs more over time effects, the instant ones are just horrible and feel spammy in combat. I know they have "lingering" types, but I feel like all of them should be over time while lingering should mean it lasts for an even longer period.
Control issues have been ranted about already. Basically just needs more customization options for PC period, we need to be able to bind sets of weapons and spells and so on not just individual items and spells and we shouldn't be limited to only the 1-8 number keys.
Scaling has some issues, can't say I know a clear way to improve it without affecting the players who want to complete the main quest straight away without getting to higher levels though. I think health scales too high on human NPCs though, bandits should not be more durable than dragons ever. Some enemies just shouldn't scale as high as they do. Non-combat skills affecting scaling just seems unavoidable, I think the only solution is to tone scaling down in general and put more caps on things. Also could make higher difficulties set a much higher minimum level for dragons.
Movement needs to adjusted, backpedaling is too fast as is strafing, and it's a little too easy to dodge enemy attacks. Terrain is also too easy to abuse, common issue with TES games it seems, not sure if it's worth whatever effort would be needed to fix it.