Crossovers for the sake of blending two unrelated continuums, hoping that fans from each will embrace it and then buy into that other continuum.... spoils each continuum. The story continuums have to be related or make sense within each other's "comic/world".
For example, the Mars Attacks crossover was pure "fiction" in the realm of Transformers, so as amusing as it was, it doesn't add anything to Transformers, and was probably ignored by the more serious/committed story fans as being the joke it was.
The Avengers crossover unfortunately was part of IDW's TFs universe (due to certain elements that carried over to and from the AHM series), but shouldn't have been, because if the Marvel superhero universe existed in the TFs universe, where have they been all the rest of the time the Decepticons were taking over the earth?
Similarly, the Spiderman cameo in the original Marvel series was also a marketing ploy to get more people crossing over to Transformers... but it begs the question, why didn't any of the Marvel Superheros ever show up during the years afterwards. And I guess the same could be asked about the GIJoe team, even if it wasn't in their jurisdiction to get involved, surely some of the cataclysmic events would warrant past allies to lend a hand to the Autobots (theoretically... but obviously not practically in the scope of the separate comic lines).
Personally, I think that crossovers should remain fantasy scenarios, separate from their respective continuums.... because either they are always of the same universe, or they stay separate. Otherwise, unless they can be plausibly explained as being definitively separate (like being on different worlds, eg, Eternia and Etheria), no matter what happens later on, you'd be wondering why they haven't rejoined forces when in a time of crisis.
That way, you can enjoy them for the creative one-off concept that they are, without thinking about where they suddenly disappeared to in the next crisis... or have to acknowledge them at all if that is a continuum you don't even like.
(and even more personally, I'd love to see a Transformers & MOTU crossover... specifically in a fantasy situation so that it doesn't upset the canon of either universe... but that'll never happen, even if IDW had both licenses, because Mattel and Hasbro would never agree to it)