I don't expect the Rachni thing to be a huge deal in ME3's story, but I was hoping that it could have an impact upon the ending. Something like this:
Shepard is willing to sacrifice himself at the end of ME3 to stop the Reapers once and for all, but if you spent the first two games making the right decisions, Shepard survives. The right decisions would be saving the Rachni, saving the Council, stopping the Geth/Quarian war, and allowing Cerberus to investigate the Collector base. If you have three of those things, the odds swing in your favour and Shepard survives, but if you only have two or less, Shepard dies. I think something like that would be a great way to have all three games tie-in with one another, it would be awesome if my decision to let the Council die in ME1 (because I was pissed at them over the death of Kaidan) is what causes my Shepard to die in a game released 4 years later. It would be a great incentive for people to replay the trilogy in order to the combination right.