My "experience" has been basically using Construct Classic and Construct 2 since, well, Construct Classic was fresh off the shelf. It's been a few years now... and before that I was using products that "inspired" the creation of Construct - mostly Multimedia Fusion 2.
I then began to bumble through things, and ask a bunch of super annoying questions to the people in-the-know. Essentially... I learned by screwing things up and asking for help (a bit like how you're asking for help). I also just read through topics in the help forum and took notice of the results that people posted - basically if I thought "Hey maybe one day that might be a useful thing to know about" I just read through it and even saved the example capx files for reference later on.
So anyway, I will take a look at Quad Tree stuff as well (I know a 'little' about it, but I will see how it maybe applies to Agar.io) and check what the boids plugin can do as well. I think boids should work fine with the proper adjustments to the boundary thresholds.
No promises on time-frame though... as again this evening I have plenty of work to complete. I haven't even worked on my own project for almost a month now, so I will take a look again as soon as time permits.
Cheers!
*EDIT*
Updated capx on post 1st page. Added boids with some quick behaviour settings and they behave pretty neat now. Try to make a big one (like 400 mass) and then separate into a few "blobs". Also set the wait timer to longer (like 10 seconds maybe). They still overlap a little in certain circumstances - but it could look cool depending how you "dress" the plain circles up. They'd look awesome if they slightly overlapped if they were made to look like some bubbling gelatinous goop.
~Sol
Please update the link.