Parallels, leaving out spoilers:
1-The Quarian fleet and the Colonial fleet. The Geth and the Cylons.
2-Tricia Helfer's Six in BSG and EDI in Mass Effect clearly have some parallels. This was not a coincidence, given the casting.
3-Both stories focus on conflict between organics and synthetics (albeit organic synthetics in BSG).
4-Both stories focus on overcoming prejudice.
5-Picking the "green" ending in ME3 has somewhat parallel results to some aspects of BSG's ending.
-"All of this has happened before/all of this will happen again." Both BSG and ME focus on cycles of violence between organics and their creations, and putting an end to those cycles.
Thank you, @Shagger.