The "clean" design choices can only go so far.
DotA has some unique abilities that are outright broken, but they can destroy your own team if used incorrectly.
A hero called Omniknight has a targeted spell-immunity skill. It gives complete immunity to abilities (some skills go through it but most do not) to the targeted ally or enemy.
So it can save an ally from an enemy caster, it can prevent an enemy from getting healed, but it can also prevent an ally from getting heals/shields etc, or save an enemy from your team's spells.
That kind of skills are common and they dramatically increase the skill cap of the game. You can't just press all your buttons and hope for the best, knowing that pretty much all of your skills will either harm enemies or benefit allies.
This kind of design allows for more power put into the skills, since they aren't 100% beneficial for the team. If Lamb's Respite (Kindred's ulti) were allies-only, it would be gutted. It would be absolutely broken. But now, enemies can play around it. They can enter the area to receive the benefits, they can bait it so it helps them more than you, they can push you out of it and completely turn it against you.
There are many ways to play around such powerful skills, simply because they're not "allies only" or "enemies only".
Of course I don't think Riot will ever design a gigantic delayed AoE nuke that can kill both allies and enemies. Like DotA, team-neutral design works best with team-neutral skills ( = utility).
Damaging abilities will always target enemies.