Regarding the post 50 skills -
Precise Touch is amazing. Let's do some math:
Each inner quiet stack increases your final BB's quality boost by 80%. A Hasty/Basic/Precise Touch does 100% quality gain by itself, so Hasty/Basic becomes 180% where Precise becomes 260%. 50% is a substantial increase for free. The math on this claim: Each stack increases your Control by 20% of the initial base. Each stack also increases the final BB by 20% because that's how BB works. BB will be under GS, so all gains are doubled. So, if your 100% for you is 100 Quality gain (if a bare Hasty/Basic gives you 100 Quality), if you have IQ9 (8 stacks), you have a (8*20+100)=260% BB. The Control boost from IQ is 20% per stack, so 8 stacks is a 2.6 multiplier, making that BB 676 instead. Throw in GS, and now you have 1352 quality gain. If instead you had IQ10 (9 stacks), you have a (9*20+100)=280% BB, control boost of 2.8x, BB=784*2=1568. Looking at IQ11 (10 stacks) - 300%*3*2=1800. Ow, wow, my earlier claim was wrong. Each IQ stack is 200% (of base) from IQ8-IQ9, 216% (of base) from IQ9-IQ10, 232% (of base) from IQ10-IQ11. Consider that a Basic Touch with, say, IQ6 is 200% (of base), that means Precise Touch gives about twice the quality gains of Basic Touch. More that twice at IQ stacks under 6, a little less at higher. That's a little simplifed because it doesn't account for the 40% (of base) boost to all touches between that one and the last one that Precise gives, versus only 20% (of base) from Basic/Hasty. That boost is about 20% if you go from IQ6 before to IQ10 by the end (since we already factored in the last hit). Now, if you were to use Precise Touch at IQ1, it would give a bonus of 120% (of base) from the extra control gains to all intermediary touches. Of course, the more you use Precise in a single synth, the less these intermediary gains are (-20% for each subsequent one), but since you only get ~2-3 Goods per 30-40 step synth, that's pretty moot.
Now, let's value an extra step at 30 CP, which is about what it costs (30.7 for MM, 29.3 for Manip, 28 for WN, 26.7 for MM2). Hasty is an 80% action. Precise is a 100% action. Let's say you're at IQ4 and hit a Good, and you are going to end on IQ10 without Precise (IQ11 with). Precise gives you, by the math above, 216(IQ10)+232(IQ11)+100(base)+50(Good)+60(IQ4)+30(Good)+200(IQ6-10)=888% (of base). Hasty not on a Good gives, by the math above, 216(IQ10)+100(base)+60(IQ4)+100(IQ5-9)=476% quality gain, so an expected gain of 380.8% (of base). If you use Precise Touch at the point mentioned, you spend 18 CP to gain 888% (of base) quality. If you hit a Good and use Tricks instead, you gain 20 CP. If you then spend 38 CP on more steps for more HTs, that's 2.27 HTs for the same durability/CP cost as the Precise, for a gain of 863%. Hmm, actually, having done the math out, that's not nearly as amazing as I had expected!
However, Precise does still have an advantage over Tricks/Hasty - there are many times where using a Tricks on a Good is sub-ideal. You're in the middle of a WN/WN2 and can't afford to use an action that doesn't consume durability. You have 1 SH2 stack left and you're at 20/70 durability. You've just used SH2 and have exactly 20 durability to blow before running your GS/Inno/BB finisher (in which case you use Precise instead of Inno if you don't have the CP for both - they cost the same, but Inno = 100% (of base - 50%*2(Great Strides)) where Precise = ~220% (more if you factor in the 100% vs 80% factor)). You get an Excellent too early to BB finish it.
So, in conclusion, if you do the math, Precise Touch isn't that amazing since it's about identical to using Tricks/+Durability/Hasty, but there are still times where it is definitely worth it to use it over Tricks.
Now, Muscle Memory, the Name-brand skills, and Maker's Mark are all really nice for progress gains. They will save you multiple steps or lots of CP depending on what you're comparing them to.
The rest are not so good:
Let's do some quick math on Innovative Touch: Assume IQ10 end, IQ6 current, IT = [100(base)+100(IQ6)+60(IQ7-9)+216(IQ10)+120(Inno*0.8)]*0.7 = 417.2% (of base) for 8 CP. HT = [100(base)+100(IQ6)+60(IQ7-9)+216(IQ10)]*0.8 = 380.8% (of base) for 0 CP. BT = [100(base)+100(IQ6)+60(IQ7-9)+216(IQ10)]*1 = 476% (of base) for 16 CP. So, IT is actually pretty bad because of the low success rate. I wish it was 0 CP or 80%, then it's be worth it (at 50% success, it'd be just as good as BT (476.8%), but half the cost).
Byregot's Brow is useless. Not only is it worse than Blessing, it requires a Good, and the Good proc rate is 5-10% for the level 60 crafts (instead of the 25% it was from 1-59). Relying on getting a Good for your finisher is really, really dangerous.
Byregot's Miracle is interesting, but it sure doesn't look good. I'll have to do the math on it later.
Whistle is terrible because you only get ~2 Goods on average on a 30-40 step synth. If you get 2 Goods, CP: 36(Whistle)-15(Satisfaction)+18(Nymeia's Wheel) = 20 Durability for 39 CP. That's pretty good, but not amazing. Of course, if you get less than 2 Goods, you've spent 36 CP for nothing, or 54 CP for 10 Durability. But, if you get 4 Goods and Satisfy all of them, CP: 36(Whistle)-30(Satisfaction)+18(Nymeia's Wheel)= 20 Durability for 24 CP. If you somehow manage to magically get 6 Goods and Satisfy on all of them, CP: 36(Whistle)-45(Satisfaction)+18(Nymeia's Wheel) = 30 Durability for 9 CP, which is pretty amazing, but that's all that Whistle does, and it's a huuuuge gamble.
Trained Hand is terrible. 150% Quality and 150% Progress at 80% for 32 CP? That's an Advanced Touch and a Standard Synthesis for the price of a Standard Touch, which sounds nice, but when would you ever use a Standard Touch in an endgame synth? The equal stacks requirement on it is also really prohibitive, and you can't control when it comes up. Progress gains for endgame synths without Ingenuity II up are minimal at best, and since Name-brand skills do more when there's less progress, the majority of whatever small amount of Progress gains it gives would be lost when you get around to using your Name-brands. It's just bad.
Heart of the Something is the worst skill of them all. 45 CP (and 25 Blue Scrips) for an increased chance of Goods for 7 steps. I have no idea what the increase is, but plenty of people have reported 0-1 Goods during those 7 steps. That's an expensive gamble. I guess if you thought crafting didn't have enough RNG, this is the skill for you?