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.
That's really the point. There is no "origin/lore" creation in ME2, so you're stuck with the choices they presume to be canon. So you have a situation where either the ME3 storyline will be kind of limited for PS3 users or there are no consequences for your choices in ME1.
You have some random character show up and tell you that the queen is important, but I get the sinking feeling that nothing of consequence will happen. Heck, at this point I don't think they'll let you choose between the 15 (or however many there are) possible party members that you've amassed throughout ME1/2.