I've not been to the Board in a few days, and the one time I was, computer problems cut out my response before I could send it to you. As such, I've had to shorten it, because I don't remember all of the response I lost, which is a shame, because I had a really great metaphor I can barely remember any of now.
Your theory is possible, conceivably, but it doesn't mesh well with the way Pokémon types are represented. Pokémon types, while in practice more active, serve to balance each other out, to allow for an individual Pokémon's moves and typing to affect a wide range of others to keep the more powerful Pokémon in check and to allow the Pokémon themselves to maintain an order to their battling style.
On the contrary, Bakugan attributes don't seem to serve to weaken or balance the power of the Bakugan, but to strengthen it, especially when the presence of multiple Attributes allows the Bakugan of the two different attributes to gain more G-Power during the extent of their working together, and then when the team-up is over, both return to their former levels.
Pokémon operates on a level where stability is the final goal, though along the way there is possibility for brief fluctuation, and Bakugan operates by maintaining stasis between battles, and then generating enough bursts of power through Abilities or Battle Gear to defeat the opponent, which makes the main point of a Bakugan battle not planning, as it can be in Pokémon, but giving yourself enough of an advantage over an opponent.
Essentially, the themes of each are so different that saying "it was the same all along" would be more than a little jarring.
It's almost order vs. chaos, were that concept not so used as to be practically a cliché. It even reflects in their evolution methods. Pokémon evolution takes place within a rigid framework; introduce this Stone to this Pokémon at this time, allow this Pokémon to gain experience (or have a certain amount of personal determination, in the anime) to this amount, introduce a Pokémon to this location, and evolution results. Bakugan, on the other hand, rarely evolve when not exposed to specific energies, and evolve in a comparatively erratic fashion, developing new powers based on the situations that they encounter or the energy that they absorb rather than following the more structured basis of the Pokémon development.
Aaand that was only slightly on-topic, but thinking of it gave me a good idea for how to mesh your idea with the one I came up with in the response I lost.
Since only a few Bakugan characters enter the Pokémon continuum, rather than the other way around, this means that their realities would have some way of crossing between each other. I'm not sure how, since I don't know the context, but I'm taking a wild guess that it may have something to do with the Reverse World, since it's the most dimensionally unstable location in the Pokémon animeverse and would be the most likely cause of non-synthetic dimensional gateways.
Anyway, once they enter, something within the Pokémon reality initially doesn't accept the Bakugans' presence. It may see it as an interference, it may see it as fundamentally incompatible with the world, it may just simply not have the same characteristics that allow Bakugan to access their full power in their home reality, what have you. Either way, they would not be able to leave their ball forms initially. Plot points kick in, though I can't provide specific suggestions since I'm not sure which eras of Bakugan and Pokémon anime you're working with, and the Bakugan develop the ability to leave their ball form at the cost of developing characteristics of Pokémon-continuum natives, which would include Pokémon typing and possibly access to certain Pokémon moves.
As hybrids (or perhaps the Bakugan could treat this as a new stage in their evolution, which could allow it to be shed as soon as they evolve again), they would still be able to use their Abilities and some of their Battle Gear, albeit through the Pokémon world assigning move types to said Bakugan items to allow them to remain compatible, but the more Bakugan-specific powers such as Gates would be inactive. This would cause the Bakugan characters to need to adapt to a new style of battling and allow their partners to change in a new way, and allow the Pokémon characters to see the Bakugan battle style without one battle style completely trumping the other, while the Bakugan would utilize moves and techniques that the Pokémon world had never encountered before.
It's not a finished idea by any standards, especially since I don't have a lot of details and either way you'd be the one to choose what parts of it to keep and which to discard, but I think it could look good with a little polishing.
What do you think?