Which set is most effective against shields and armor?

Best combo I've found to deal with everything is Shield Drain, Incinerate and Revanant VI. You can't beat combo damage currently. SD an Incinerate literally works in any order depending on what you need. Revanant draws fire and over it's life span will arguably do more damage than any other skill which also frees up time for you to just shoot, plus it can combo with your team mates or your own skills. Boom!

But aren't a lot of biotic abilities only for unshielded and unarmored targets?

Biotic abilities can be upgraded to target shields and armor as well. Biotic passives also plays a role, for example, target affected by Biotic takes 20% more damage from all sources.

Actually I dont like to use them against unprotected enemies because they fly all over the place... I have to run all over the place stomping on them 

Shielded and Armored enemies I like, they will stand there and die without troubling me