You should be able to get ~1500 faction everyday in Mechagon, 3k+ now with the bonus. It usually takes less then 20 minutes which is nice:
1. Get the jetpack (blueprint drops off of rustfeather & beastbot)
2. On Chromie days, go to the other timeline and farm the personal time displacer blueprint (drops off of clockwork giants).
3. Go to Mechagon in warmode (even if you don't like PvP, it doesn't matter). There is a PvP only prototype quest. Pick this up and fly around mechagon on your jetpack. Just fly around looting chests, you can loot them in the air on your jetpack, so you never have to dismount. The risk of getting engaged in PvP is very low, and if you do 99% of the time you can just fly away if you are worried about PvP'ing. This quest gives 200 faction normally (400 now), and is very easy, so it's nice to do. Killing rares also yield a lot of prototypes, so kill them when you can in warmode.
4. If you've gone around mechagon and don't have 150 prototypes yet for the PvP quest, use your personal time displacer to go to the alternate timeline. On non-chromie days, this place is usually empty. You can easily kill The Arachnid Harvester (Mount drop chance) & The Rusty Prince for 30-40 prototypes per kill (they are usually up in the alternative timeline in Warmode). Doing the quests here & getting chests in this timeline also provide prototypes. There are 2 quests, you pick up the first, and once you complete it, it gives you a 2nd quest. Do these daily. Don't do the vaultbot quest in the alternate timeline (you can if you want but it is more involved and not worth your time in terms of faction).
5. Once you've completed the PvP quest, go to the mailbox area in Mechagon. It is a very tiny rest area. You can turn off warmode here if you like. You can now complete the rest of the dailies, and ensure you've completed the main daily as it yields the most faction.