It did annoy me in ME 2, but that is compounded because my the need to install the discs to keep the noise and loading times down (though not after deaths for some reason), but I will live
I would chose 1 install over 2 installs and 2 discs, but of course the 2 installs are optional. But yes, if you have the option, the blu-ray is preferable, but it isn't a huge deal