When we speak about these two zodiac signs, it's important to remind ourselves of their differences and similarities, here's a short observation:
Similarities: Both fixed
Both stubborn
Both enjoy mind games
Both somewhat quirky
Differences: Scorpio is jealous - Aquarius isn't
Aquarius is detached - Scorpio isn't
Scorpio wants one love affair forever - Aquarius is petrified of that
When these two sun signs meet, it's a battle of wills, the Scorpio like to poke and prod. The Aquarius also likes to do this, but in a more lighthearted way, where as Scorpio can sometimes be fueled by repressed bitter feelings. Here is where the difference lies, the Aquarius mostly deals generally in a grand scheme, the world is Aquarius playground, and they very much would like it to be better, and if it isn't what they want, they will go to great lengths to make it that way. Very unselfish in these aspects, however the Aquarius can also be a bit selfish in the way they go about these things, sometimes letting their emotions get the better of them, ironically for a cold and detached sign, these guys are very prone to suffer from disenchantment with society from time to time, never succumbing to it fully though.
Scorpio plunges deep into emotional waters, that they live in and have lived in from birth, the catch is that they will not open themselves as an Aquarius does with his heart for societal justice. Aquarius perceives this as indifference and even though Aqua can be the master of being indifferent, they rarely will put up with anything they see as selfish or unneeded and childish, ruled by Saturn and Uranus, they have a dose of seriousness as well as open hearted (to the world) excitement. Scorpio rules in secrets, games, and passion, Scorpios games play on the emotions, the mind and sometimes cruelty to others. Aquarius not only does not respect this, but they hate, and I mean hate any person they see as keeping someone else down.
Of course, what Aquarius perceives as selfishness from Scorpio isn't always so. Nothing is truly as it seems with the Scorp, and though Aqua does enjoy puzzles and the like, they won't put up with games that they see as childish and immature schoolyard bullying. So the ultimate clash lies in the fact that Aquarius is not so much into personal ventures as the Scorp is and also the fact that Scorpio cannot relate to Aquarius much at all, because Aquarius is a very large broad scope, and Scorpio is much more of a silent hunger, and even though they may be similar and want change for the world, Scorpio readily accepts that the world isn't perfect.
Aquarius would tell the Scorpio to get over it if they heard them complaining about what they see as a selfish complaining and distraction from the bigger picture that Aqua believes everyone should contribute to and if you aren't contributing you are damaging. This of course is not true all of the time, and a bit unfair for the Scorpio to be victimized based off of perception, oh but the thin line you tow Scorpio because you do this exact same thing sometimes. Anyways, to reiterate my previous statement about Aquarius telling the Scorpio to get over small minded strife and hurt emotions, the Scorp would tell Aquarius to get over trying to save the world because it is a dark place, and there's nothing anyone can do about it, so deal with it.
Scorpio understands darkness and the twisted intent from people, they bluntly tell people how they should be, and what they should do - Aquarius doesn't like this, they hate constraint placed on them by some controlling person - The Scorpio. So the difference again lies in the fact that Scorpio hits people personally, while Aquarius when they tell people what they should be doing they just offer advice, and they also persuade the person to do humanitarian things, not personal attacks. Aquarius has little time to be bitter about someone or something, and plan revenge or hack away for years at them about something minor (in the Aqua mind it is minor).
Usually, the only time you'll see an Aquarius angry or distraught is if they are feeling like humanity is dying or that someone isn't pulling their weight. Scorpio does everything in that manner, everything they do is either happy or sad, mad or content, this or that. Aquarius find this somewhat cumbersome and boring, also they might perceive this as a falsity but it is not, the Scorpio is dead serious. Still though, the Aquarius can't help but feel like it's a minor thing and that they'll get over it, the thing is they won't get over it, and this annoys the Aquarius to no end. The way Aquarius sees it is - put up or shut up. While Scorp may also preach this, they rarely do it - sorry Scorpios. Aquarius feels very much larger than a Scorpio in scope and in life in general because they feel like they represent humanity, while they see the Scorpio as representing themselves only. Even if it's not true, Aquarius usually goes on instinct, and if they see someone with a selfish bone in their body or a bad negative aura like Scorpio usually carries, they will back away. If there's one thing Aqua hates more than injustice is bitterness and negative energy.
In the end Scorpio feels like they usually do, victimized for being too emotional and misunderstood, Aquarius feels the same way but they feel it as society betrayed them, where as Scorpio feels like Aquarius betrayed them.
In the end neither sign wins, both believes they won and will continue to believe it.
Peace of mind goes to Aquarius, however.