Balancing a crossover with Space Battleship Yamato 2199/2202?

So, say if I wanted to make a crossover with SBY 2199/2202, which I’m not (at the moment), but I didn’t just want it to be power wank (seriously, the Yamato alone could probably wreck the Citadel Defence Fleet, especially with the Wave Motion Gun). How would I go about doing that? And before you ask, I already have a few ideas…

1. Have the Reapers and the Protheans kill each other off. This scenario is actually inspired by the IBO crossover fic Bad Things Coms In Twos, and a consequence is that the ME races have a significant tech boost compared to canon. Probably the easiest option, to be honest. 2. Get rid of a part of SBY’s tech tree, for example their warp tech, or hell, even the Wave Motion Gun itself. The problem here is that you have to be careful, or you get rid of everything about SBY that made it ridiculously cool. I mean, do we really just wanna see the Yamato firing regular shells? Don’t get me wrong, it’d still be cool, but it just wouldn’t have the same “oomph” as the shock cannons do. 3. Just…don’t include the Cosmo Force. There are still a bunch of cool ships from the series you CAN use instead (I have a soft spot for the Garmillas carriers, you know, the ones that have the three launch decks). You could just plop in the Garmillas in ME canon with a bit of finagling, and the tech disparity would be better. Not completely solved, but better. The obvious downside would no Yamato. Could you finagle it in there? Maybe, but it’d take a bit of handwaving and personality changes (ie: Dessler not planning to drop a station on his own planet. Oh, and less conquery and genocidey. Actually that’d make them more like the Turians…huh. Food for thought) to do it.

So? Thoughts and ideas? I’m genuinely curious about what you’d guys do to balance the two franchises.