If you can’t alpha strike, you are not alpha striking right 
Though I’m not doing it in this playthrough, I did in my first one as I was experimenting with different builds/strategies.
The single most reliable way to do it is with a sniper, or assault with the strongman perk. Let’s call him Roy. Roy is a sniper with that perk. I will dual class him into assault and give him a deceptor, leg mutation that gives him +5 to speed, light anu armor that gives him + 3 to speed and the synedrion sniper helmet for 25% accuracy bonus. I will give him top speed and high willpower, dash, quickaim, rapid clearance and ready for action. I will bring along a priest with frenzy and assaults with rally the troops in case there is any trouble closing rapid clearance loops. Oh, if I can, I will bring Roy’s twin brother or sister with him. If I’m not feeling confident, both his siblings.
On a mission, Roy and his siblings, after the Priest casts frenzy, can dash to any point of the map, execute any crab or Triton (including elites), or non elite sirens with a single shot at 5 tiles distance. Bunch of them together with Return Fire? All the better.
Can Roy clean maps all on his own in one turn? Yes, sometimes. But he doesn’t have to. I still have my heavy bombards, my monster-killer with rage burst/infiltrator that does 300% damage with each shot and is a serker too so he can do this nuking four times a turn…
Now with the DLC there is this new thing - the bionic torso to do melee attacks for 1 AP. Put that on an assault/heavy (with extreme mobility) and right there you break the game. (In my current playthrough I gave this torso to a sniper/heavy, and she is still absolutely devastating, one blow killing any crab or Triton, but at least she doesn’t have rapid clearance).
Bottomline: I wouldn’t know how to stop Roy and his brethren from alpha striking. Maybe enemies starting on overwatch, like Spite suggested from the start, but then there are already these new bionic legs to ignore overwatch. Also, it would have unintended and very annoying consequences in some maps, like nests.
And then, TBH, I just don’t see the point of having Roys in the game at all. It’s not like on turn 2 they will stop breaking the game.
In conclusion, I think some serious nerfing is absolutely necessary to get rid of alpha striking, or risk free alpha striking if you will. Then some elements might be introduced/enhanced/optimized to make first turn attacking a viable, but risky tactic.