I have a couple issues with Sofia. I do like that you considered her weaknesses and cons, but Sofia is a little too spread out.
Looking at her classification:
TYPE: AP DPS Assassin, Ranged.
I am already worried.
Assassins usually have the weakness of being low range, so that if they want to burst you they have to get up close and personal which is riskier. Now ranged assassins aren't impossible to design well, but its difficult. Leblanc is an example of a ranged assassin, but you'll notice even she has to get close to her victim with her W.
Sofia however has no mechanic like this. The only incentive to stay near an enemy is her ultimate's delay.
You did mention she has low range. However one would hardly ever see Sofia playing the risky playstyle assassins do. Most likely she would just be an extra bursty ranged character.
This issue gets worse when you give her the ability to DPS as well. If Sofia plays safe and doesn't go for an all out burst playstyle, she has safer DPS to fall back on. If you want Sofia to be the assassin she was intended to be, there needs to be a risk and reward mechanic.
I would entirely remove her DPS. Assassins are supposed to fall short in this regard and have bad damage after they blow their combo. You take away a significant weakness by giving her burst and dps.
Passive - The Grave's End: Sofia's basic attacks on enemy champions reduce all of her dead teammate's death timer by 1 second.
While its a neat effect, playing with death timers like this sounds like it goes two ways. Either the ability is tuned so strong that enemy must actively stay away from Sophia to prevent her from bringing back her allies sooner, or the ability is tuned weak enough that enemies don't bother.
I don't see a possible middle ground where enemies aren't too afraid of getting basic attacked, but it still feels effective.
The other issue with this spell is that it is very counter intuitive. The time when you want the spell is not the time you should be using it.
The passive is best utilized when Sophia has many dead allies. Well when a squishy ranged like Sophia has any number of dead allies, she should be playing safer. This isn't a good way to encourage Sophia to play risky, because this is when the game's core design says, don't play risky.
Further more, this ability is often going to just do nothing. If her team is stomping the other one, she is probably not going to have many death timers to reduce that game. If her team is losing a lot, she is probably not going to go auto attack that Yasuo while her support and jungler are dead.
Finally this ability just doesn't fit her playstyle of being a damage focused assassin.
Q - Soul's Revenge: Sophia Fires a Black-Colored Soul (same hitbox as Lux's Q, just a bit faster) - Which deals 70% AP damage to all enemies it passes through, slowing them. She then gains Movement speed and Invisibility according to how many champions she hit with this ability (1 second for 1 champion, 2 seconds for 2 champions etc).
This is a pretty cool spell. I like it and it not only rewards her for creative use of it, but it also enables her as time goes on. While many assassins struggle in team fights, Sophia alleviates this a little bit by gaining additional stealth time if more enemies are present.
My only criticism would be to increase the base stealth and give it reduced consecutive increases. What I mean by that is the first enemy hit grants 1.5 seconds of stealth, the second .75, the third .5, the fourth .25, and maybe the fifth .25 as well.
What this does is it makes her Q stealth good when there are only a few enemies, but still gets better when there are multiple. Because if you have a flat increase per enemy hit (1 second) than your forcing yourself to balance the ability with 5 second stealth in mind which will usually never happen, but could. Kalista E has uses this same mechanic because it makes her E feel better when she uses it at a low amount of spears, but still makes it sub optimal.
W - Dark Energy: (PASSIVE ABILITY) - Sofia's Autoattacks become stronger as she autoattacks enemy champions. Her first AA on an enemy deals normal damage. Her second AA deals 20% AP Extra Damage. Her 3rd Autoattack deals 30% AP Extra Damage. Her 4th AA on an Enemy champion deals 40% Extra Damage and puts this ability on a 3 second cooldown.
A relatively boring ability to me but thats not necessarily bad. What is damaging to the kits overall design is that your giving a ranged assassin consistent and solid DPS. Azir was very difficult for Riot to balance without kit changes because he did too many things. Sophia does a lot of things too (she can DPS, she can burst, she is mobile, she has stealth, she has true damage, she has utility, etc.).
E - Rush of the Dead: Sofia dashes to a target location (dash range is slightly less than Kassadin's R); can be reactivated again within 2 seconds (35/30/25/25/20 second cooldown
Its a fitting ability but it feels more like a weak ultimate. Its in this weird limbo of being really strong for a basic ability but too weak to be an ultimate. I'd just reduce the cooldown and nerf the range.
Also the two second window would feel really shit to use. Certainly increase that window so you have more time to reactivate it.
R - Demonize: (Kennen-Ult sized raius) - Upon activation, all enemies within this radius are slowed by 20/30/35% for the next 2 seconds. Once the slow is over, Sofia deals 500/750/1000 true damage shared between all enemies affected by ult (if only 1 enemy was ulted, they take the full damage).
First off I'll say I like the damage split mechanic. Its just interesting whether or not its useful.
For this abiltiy we come back however to it not being fitting for an assassin. A 2 second AoE slow isn't something an assassin wants in their kit and having their ultimate nuke spell accidentally be spread among the rest of the team would feel pretty bad.
A must change on this ability is to reduce the base damage and give it some scaling. As it stands right now, a level 6 Sophia with no items deals the same damage with her ult as a fed level 10 Sophia. Her items play literally no role in how effective her ult is.
Finally I just don't think that most ADC's are going to be able to avoid Demonize. Assuming an ADC could reposition out of her ult with the slow attached, Sophia has two blinks to make sure they don't.
Anyways this review got a lot longer than I anticipated but I hope it was helpful. Reducing death timers isn't a totally bad idea, it could work, but I think Sophia has some things to work out first.