How was reuniting the Quarians and the Geth a tough decision?
Even if you could unite them, it was not obvious at all when Legion asks you if you want to upload that the quarian fleet would back off - or that Tali would ask you again to stop this.
I stayed in front of the screen, with the question "Does this unit have a soul", and great music in the background, for a little while. I don't know if leaving Legion's question in background (instead of 'should i go ahead with upload?' or something akin to this) was intentional, but i personally thought it was brilliant. It felt like you were ultimately deciding what the right answer to that question was.
edit: I think it's also better done than the krogan decision. In Tuchanka, unlike the geth/quarian decision, I feel you're more likely to be conflicted if you played well so far. If there are any fuck ups, say Eve is dead and Wreav leads the Krogan, I feel that helping the krogan sounds much more dangerous and I probably would have happily fooled them. If the krogan are as dangerous as history showed, in case things go well, you're relying entirely on Wrex and Eve convincing their people to be diplomatic from now on - something which they haven't really shown until that point (unlike the geth).