So what if Koggy did ONLY magic damage?
Yeah, Koggles puts out a lot of magic damage right now, but what if that were the only type of damage he dished out? Ryze had an Innate like that, back in the day. But I think something akin to it could be added to Koggy to help provide him with a more robust niche. There's a reason why the only champ in the ADC position with a lower pick-rate than Kog is Quinn. The things he does well (Tank Buster, Poke/Cleanup, Long range auto-attacker) can all be provided by other champions who have stronger early games, are safer, or both.
So why not give him something that NO other ADC offers?
(Innate) Eldritch Acid: Kog'Maw converts all Physical damage he deals into Magic damage. Additionally, his basic attacks can not critically strike. Instead, they shred flat magic resist equal to (percentage) of his critical strike chance, stacking up to three times.
Due to the new Innate, remaking the side-effect on his Q would probably be in order. Maybe make it apply an extra stack of his Innate? Not really sure there.
Either way, Koggy would be putting out pure Magic damage. It would allow him to be picked onto teams that already have a ton of physical damage and are in need of some major magical threat. It would also push him more out of the tank-busting role (he already can't compete with Vayne on that front) and more into the squish-buster role (which he was before his Q got remade, the flat resist shred was nasty). Destroying people's magic resist would also make him a valuable asset to other magic damage dealers since he would be amping their damage significantly as well.
tl;dr: Koggy needs a unique niche to help set him apart from Vayne and Jinx (and to a lesser extent, Ez and Trist). Transitioning him to a pure magic damage threat could help accomplish that goal.