One area cloaker can cloak as many units as can fit inside it's area. It can be nerfed by dynamically setting its cost based on the number and value of units being cloaked. This is how other units, like infiltrator, have been crushed in the past(15 e/s per infiltrator is insane).
We have multiple systems in place to classify different units, and we could use one of those classifications. I'm pointing at "light, medium, and heavy weight" units based on transporter pickup.
Cloaking a large army of small units should incure a large energy fee, and cloaking large units should incure a significant energy cost. Also, I think the re-cloak time nerf meant to hit lance has hit many other unit stratagies.
To put numbers to these concepts, imagine this:
cloaktime: (proximity decloak, weapon fire/damage)
Light weight transportable units(glaive, duck, bandit, rouge etc.) should cost 1.5 e/s to cloak and have recloak times of (1.5, 3).
Medium weight transportable units(jack, minataur, lance, etc.) should cost 4 e/s to cloak and have recloak times of (3, 5).
Heavyweight transportable units(demistriders like Grizzly, Tremor, Jugglenaught, goliath, and striders) should cost 8 e/s to cloak and have recloak times of (5, 8)
The energy cost theoretically is applied to the iris/cornea that is cloaking the unit. the areacloaker would then have the e/s cost of:
cost = 1.5 + 5 + 1.5(#light) + 4(#medium) + 8(#heavy)
where 1.5 is the cost of jamming, 5 is the base cloak cost, and the additional terms are dynamically allocated to what's currently being cloaked.
Edit: as it stands right now, if you have 3 infiltrators(45 e/s), it might be more economical to build an area cloaker to decrease the cloak cost to 16.5 instead of building another fusion, because when a personal cloaked unit stands in an active area cloaker it cloaks for free.