When below level 50 almost everything gives you a boost so theres no particular order. Just make sure to level up all crafting jobs to 50 before going further. After that you can follow recommendations from Upgrade Stage 2:
1. Ingenuity I or II: 38.9% to average HQ rate
2. Byregot's Blessing: 33.3%
3. Maker's Mark: 26.6%
4. Flawless Synthesis: - (required for Maker's Mark)
5. Comfort Zone: 20.2%
6. Piece by Piece: 13.0%
7. Tricks of the Trade: 9.8%
8. Steady Hand II: 6.5%
9. Innovation: 4.4%
10. Reclaim: -
Hasty Touch: 2.0%
Careful Synthesis II: 1.2%
Rapid Synthesis: 1.3%
Rumination: 0.0014%
Waste Not I: 0.00072%
Waste Not II: 0%
Manipulation I: 0%
Careful Synthesis I: 0%
Muscle Memory: 0% (3.7% when no Maker's Mark)
As you can see, the crafting system in Stormblood has reached an almost perfect balance.
The most valuable cross class actions fit exactly into 10 available slots on any crafting job. When you reach level 70 you have to setup your skills only once, and no more swapping for Reclaim is required.
Obviously you dont need Makers and Flawless until 70 so you can take HT + CS2 instead. I also dont use Innovation but thats up to you.