As was mentioned above, it looks like this issue was related to the Origin In-Game Overlay. Disabling the overlay should help with the performance issues.
Thanks everyone for bearing with us on this.
You might also try installing an Intel Xeon E5-2680 v4 processor on an X99 Motherboard that has a 2011 v3 CPU socket type. That is because this Xeon has plenty of power and plenty of hyper threads to deal with whatever you throw at it. Then too, it is a Mass Effect 3 official CPU, (as obviated by the alphanumeric part number SR2N7.) Oh, and it also can run DDR4 2400, where the E5-2618L v4 is capped at DDR4 2133 RAM. Of course, having quad channel memory access doubles the effective RAM throughput, giving me effective access to 76.8 GB/s with just 16GB installed on my system.
Okay, so, it might or might not actually solve your game running poorly on Steam problem. But, how cool for there to be a CPU out there that actually incorporates the SR2 and the N7 designations within it's part number. I thought it was pretty cool anyway, when I saw the E5-2680 v4 CPU on eBay selling CHEAP @ just $168.00. I was looking for an upgrade for my MSI X99-SLI MB, which is currently running quite smoothly overall with an 10 core/20 thread E5-2618L v4 Xeon CPU. The E5-2680 v4 actually runs at 100MHz faster for both base and boost clocks and has 14 cores/28 threads, making it a faster, and more powerful, processor. Having said that, the more likely cause of stutter and lag (in single player) is going to be with your graphics card or graphics card driver. I'm currently using an MSI nVidia GTX 1060 gaming card with 3GB of GDDR5 RAM. Using FHD settings, with anti-aliasing, and dynamic shadows enabled, I'm running perfectly using DRM enforcer Origin... which I can only guess would be equal in every other way to Steam, since the PC game mechanics and code are the same, in the very least, while in single player mode.
I know that this thread is old but since I just had this issue I have here the solution that worked for me without installing anything:
1. Make Sure Origin and Mass Effect 3 are closed.
2. Go to Mass Effect 3's folder where Origin is installed, should be something like: "C:\Program Files (x86)\Steam\steamapps\common\Mass Effect 3\__Installer\Origin\redist\internal" May vary on your installation path.
3. Open OriginThinSetup.exe
4. Disable Origin Overlay. Press the top-left button "Origin", then Application Settings, then Origin In-Game and disable that overlay.
For me worked like a charm, I could disable the overlay since I was not in-game already.
The problem was that the overlay in ME3 was always on despite being disable in Origin itself.
You could not disable the overlay in ME3 if you started the game with Steam.
That got fixed in the meantime.