Why not a little of both?
My group adds both individual pilot SPAs and Formation bonuses on occassion; so far, no bad experiences, but mileage always varies from group to group.
For Individual Pilot SPAs, we don't normally assign/allow protomechs a SPA-- they've been deemed too fragile or too "insignificant" of a unit type to be considered to be a special pilot. (Opinion). Since each Point is actually 5 units combined, we do count the Point as a singular entity for determining the number of Pilot SPAs considered (so in the previous example, 1 in 25 protomechs may receive a Pilot SPA because the ratio of 1:4 has been met, but only one time)
For Groups and formation bonuses, its different: we count individual protomechs as eligible, but any SPA assignments by Formation are assigned to the individual unit and may not be "shared" between units. This method comes with a mixed bag of good and bad.
An instance of good: a Cavalry Star of 25 Roc [Standard] (Skirmishers with speed/jump) awards 18 protos of its formation with Speed Demon (25 x 75% = 18.75, round down)
An instance of bad: a Fire Support Star of 25 Gorgons [Standard] (25 units with IF1) only 2 units in the entire formation may receive the Oblique Attacker (or 8%)
...Now, I typically run a Mixed Nova for sampling/demo purposes (3 Omnimechs, 2 Omnivehicles, 5 protomechs; choice of a star of mechanized BA). This usually translates into a 15-unit formation with only 5 eligible units (mechs and vees) for Individual SPAs, and pads the Formation bonus % with extra "eligible" by making the unit count twice as large, with the Battle armor forming their own Formation (or none, depending on the game).
For purely entertainment reasons, I have considered using the Horde (Lance) Formation (CM:Kurita p.86) for my pure-Protomech Stars, but until recently, I did not have sufficient numbers to perform such an adventure (I can assure you, my peer will be bringing artillery that day). This Formation type begs to have a bunch of little, annoying critters cluttering the field of play, so I continue to believe that the way we do it (so far) has been the correct approach: open mindedness and playful intent.
Hope you find my response in good favor.