Themes:
Humans vs. Aliens
Biotics vs. non-biotics
Politics and bureaucracy vs. agility and effectiveness (Paragon / Renegade)
Compassion vs. greed
Ends vs. means
Diplomacy vs. violence
Many vs. few (sacrifice)
Choice vs. destiny (self-determinations and free will)
War vs. peace
Revenge vs. forgiveness (redemption)
Trust and betrayal
Individualism and expression vs. conformity
Personal relationships during a time of strife
Synthetic "life"
Genetic engineering
Doing the impossible
Duty

Examples:
Quarians and the Migrant Fleet
Quarians and the Geth
Rachni Wars
Krogan Rebellions
Batarians and Humans
First Contact War
Saren
The Council
Omega
Spectres
The /Destiny Acension/
Garrus and C-Sec
The Protheans (society)
The Protheans/Collectors (fate)
The Reapers
Navigator Pressly (and Ashley to a lesser extent)
Cerberus and the Illusive Man
Kaidan, Jack, the biotic colony, and other biotic issues
Project Overlord
Kasumi
Zaeed's Revenge
Joker's disability
Joker and EDI
EDI as a life form
Geth "Heretics"
Husks (and other Reaperified creatures) as enemies
Matriarch Benezia and Liara
Ardat-Yakshi and the Asari pureblood taboo
VI vs AI (Rogue VI on Luna -> EDI, Avina on the Citadel, Shadow Broker VI, Vigil on Ilos, VI on Feros, etc.)
Conrad Verner
Barla Von
The Shadow Broker
Harkin and Bailey
Risks of colonization (Zhu's Hope, Horizon, other colonies in the Traverse and the Terminus Systems)
Business ethics (ExoGeni, Noveria, slave Quarian, Asari star charts, mercenaries, etc)
Kaidan or Ashley?
Michael & Rebekah Petrovsky (gene therapy)
Samesh Bhatia (wife's body)
AI on the Citadel (self-destructs)
Citadel Reporter (PAWNCH!)
Helena Blake
Balak and Bring Down the Sky
Mordin and the Genophage
Maelon and the Genophage
Garrus on Omega
Mordin's clinic
Okeer, Grunt, Wrex, and the future of the Krogan
The Justicar's Code
Thane and his son
Nassana Dantius
Quarians and war with the Geth
Legion
Legion and Tali
Jacob's father
Miranda and her sister
Jack and Aresh
Indoctrination

Shades of Grey