I never really had a huge problem with ME's scores in the latter two games because for the most part it always felt thematic; the Geth, the lion's share of your opponents in ME1, were synthetic. Saren had been heavily synthetically modified, and Sovereign of course was a machine. The score is electric and matches that.
In ME2, the Collectors are organic, and when you're fighting them there's a generally more organic, orchestral style score. However, when you do fight the Geth in that game, such as Tali's missions, the sound takes on a
very similar tone to ME1 and even rearranges some recognizable tunes from that game.
ME3 is a similar sort of thing, really - all the mish-mash enemies you fight are twisted organics adjusted by synthetics, but certainly not like the Geth. ME3 probably has the least identity in its audio, but it never felt out of place to me; it felt like the score was pretty consistent in a thematic sense.
Heh, I forgot about music heavily featured in all 3 games, but you're right. Technically I suppose it counts as ME1 music, just like Vigil.
There's also that theme that plays when you're becoming a Spectre which is more or less "The Mass Effect theme". It gets remixed for when your ships are showing up for Priority Earth in ME3.
It's more difficult to recognize, but that theme is the basis for 'An End Once and For All' in ME3 as well. I always liked how ME2 and 3 never directly use that theme, but use the base and then deviate from it. I felt that was a nice touch.