Not gonna lie this in combination of 2000h sounds like you just want to brute force everyone with the same default build.
From my limited <300h in the game I kinda think this game at a higher levels is all about strats and counter strats less so about aim. I would guesstimate that priority list goes like:
1. strat / anti-strat
2. movement / dodging
3. aim mechanics
As said in my comment above - Graves got totally destroyed by 3 lunges (basically lost 3/4 of health). Imo clear sign that build was totally off for countering / taking Apollo 1v1.
So for you same as anyone else there are clear 3 choices vs Apollo (or to be fair any other hero):
1. follow during the game what enemies buy and counter-buy accordingly
2. ignore point 1, go with your build but then see which heroes you can take 1v1 and which you MUST avoid and/or take 1v2 or even 1v3
3. ignore point 1 and 2 = just get rolled over as soon as you have opponent that is not afraid of your build -> complain in forums
Yes, I agree that if Apollo's Ult teleports him through walls and applies damage on the other side = that is broken and has to be fixed.
If his abilities somehow interfere with incoming damage (does not seem to be the case for me tbh) = yes that needs to be fixed. But this might be also server issue which I think is a big issue in Deadlock, Valve probably not spending top $$$ for free to play beta testing. Fair game.
Still all of the above is 90% people inability to counter Apollo builds aimed to decimate nubs, 10% is game mechanics and stuff imo.