Metahumans use Intuition + Perception[Mental]
Drones generally use Pilot + Clearsight[Sensor]
Remote/VR use Intuition + Perception[Lower of Sensor or Data Processing]
Jumped in use Intuition + Perception[Sensor]
You can use Electronic Warfare instead of Perception when using sensors, too... (CRB, p.445)
So spotting a mini drone roll your check modified by (here comes the confusion)
CRB p.135/136 chart - Obscured/Small/Muffled threshold 3 (ok mini drone) - which leads to bizarre instance where unless you have 9 or better dice pool for pilot + autosoft, statistically don't use sneaking unless the threshold stacks with the net hits for sneaking in the opposed roll.
As already said, you should only use that treshold table for unopposed tests.
And the very broad categories of large/normal/small/micro used in that table don't match the corresponding drone sizes at all.
Given a contact lens is listed as an example of a small item, i would not use a treshold of 3 for anything short of a micro drone, if at all. And small drones like the Lockheed Optic-X2 ("size of a large hawk") or the Horizon Mini-Zep (which is used to display ads on it's airbag’s surface) definitely don't belong in the same "small" size category as that contact lense.
Then these unopposed perception tests cover two different cases: Noticing something you are not actively looking for or looking for something specific. In the first case a treshold of 2 for a minidrone the size of a real life pigeon or a human (cyber-)hand (to use two examples of mini-drones) sitting on a desk in some room you just entered seems reasonable. People miss all kind of obvious things. If you actually enter the room to find that drone you already get +3 dice (see: Perception test modifiers) and it gets really hard to miss it with an average intuition stat and at least some perception skill.
(Btw... The act of looking for that specific mini-drone prototype they are hired to steal, should be handled as a teamwork test (CRB, p.135, last sentence) instead of letting everyone roll to see who finds it.)
CRB p.184 chart says -3 dice penalty for drones (unless micro) drones/vehicles sensor test (I assume this also means using them in remote AR/VR and jumped in)
I'm pretty sure that table is only meant to apply to sensor targetting, which uses a different mechanic (Log+Gunnery[Sensor] instead of Agi+Gunnery[Accuracy]) to represent a different way of using sensors/vehicle weapons (primarily) in vehicle combat instead of the usual remote-controlling approach.
Rigger 5.0 p.181 chart (and middle paragraph directly to it's left) says -2 dice penalty for mini drone size
That's the table to use for perception, shooting etc. for basically every test opposed by a drone, based on it's size.
And i would include perception modifiers (CRB, p.135) or at least visibility/light environmental modifiers (CRB, p.175). They are (as of combat rules) automatically included if you try to shoot the drone, so why not use them for spotting it, too?
So what's the final threshold/penalty to the observer(threshold + size mod, or one or the other)?
Rolling to see if you noticed that (inactive) minidrone sitting on a desk: perception test modifiers (including visibility/light modifiers (from CRB, p.175)) vs a fixed treshold depending on size (more 2 than 3, if you asked me...)
Rolling to notice that pesky fly-spy following you: -2 dice penalty from size and perception test modifiers, opposed by drone and no treshold required...
(And yes, these modifiers include free +3 dice for players actually mentioning that their characters are watching out for such things. Nothing's wrong with a healthy dose of paranoia
)
Edit: But please don't ask about speed (on top of size) modifiers from Rigger5. I could never figure out that example and i'm still pondering how a speed 2P Dragonfly moves at speed 3 and does speed (3) + half body (1/2 = 0.5 ≈ 1) = 3 damage.
