I'd try to create a "Hasbroverse" franchise, with the Joes as the center of the relatively normal side and the Transformers as the center of the cosmic side. Of course, characters from the cosmic side wouldn't appear in stories of the normal side, just like super-powered DC characters don't appear in Batman comics.
Of course, both "centers" would need more than one series: the Joes would work pretty well with the same series as in Marvel, one with advanced tech and continuity, and another with self-contained stories of more realistic military missions. Transformers should have one series set on Earth (to focus in the Robots in Disguise aspect and show cluelessness on Earth customs and another set on Cybertron and other planets, more like a space opera.
The COPs series should begin with a gang war between Big Bos' gang and the Headhunters, with the DEF as guest stars. After the end of that first saga, writers should check which DEF members worked well in the team dynamic and keep them with the COPs.
Before having a MASK series, Trakker should appear in GI Joe as a test ground for the MASK series. Since it's in the middle point between "realistic soldiers" and "fantastic technology", it would likely get a lot of crossovers with other series.
Action Man, to differentiate his stories from the Joes, would participate in more stealth and/or secretive operations with Action Force (as a mix of the Palitoy and AM rosters).
Inhumanoids should limit their actions to a specific geographic area to not disturb the realism of other series. However,

would be "transplanted" to this series with the new codename Sabre Jet, just like he was in Sunbow.
The Oktober Guard also deserve their own miniseries. Not a regular series, or they'd stop appearing in the Joes' comic.
While Jem and MLP are part of the 'verse, they wouldn't work. the idea of Mr Benton using advanced tech only to turn his daughter into a superstar currently generates some implausibility (the concept worked in the more inoccent 80s yet not today), and while the Ponies' land is technically part of the hasbroverse, they are too cartoonish to believably appear close to the others (just like, despite Disney owning Marvel, the Avengers don't meet the Ultraheroes).
Did I forget something?