Regarding controlling other units:
Short answer is it's unlikely.
Long answer! When we made League, we looked at the obvious inspiration, Dota, and made some baseline changes to the game that Dota, being a War3 mod, couldn't make. One of them is the "stickiness" of self selection. In League, you cannot "unselect" yourself as a unit, and this has a lot of positive implications, but it also means that RTS-like controls are out of scope. This is the most intuitive control scheme for multiple units.
So if we wanted to make a champ that was two independently controllable units, we would need to do a LOT of work on the UI / input side. Additionally, many skills learned on this champion would not be transferrable to other champions and no other champions would prepare you for this dual champion. And finally, because brain cycles are a finite resource, there is only so much complexity we could put into the champion's actual kit--most of its complexity budget would be eaten up already by the mere fact that you're controlling two independent units.
TL;DR: I don't think this kind of champion would be a good fit for League, but as always I could be wrong!
Source
As for more "unique" abilities, just because something is a skillshot or is targeted doesn't mean it can't be unique. We have skillshots with unique trajectory (Diana's curved Q, Vel'Koz's 90 degree Q) - I think usually the unique aspects can be equal parts the delivery system (skill shot or not) as well as the effects itself (is it an explosion? A Zone that does something? Is it a status effect? A buff? Debuff?)
Over the long term, Riot has been much more creative and flexible in terms of what they'll allow in a champion's kit. Hopefully they keep it up!
