Camwin's post is definitely the standard thinking (and is exactly the way my merits are set, including the non-PUP specific ones). You really can't go wrong with following that post.
Also, a note that even if you really like Sharpshot, automaton melee is better than automaton ranged even on SS. Why? The key for SS is generating TP to get off more weapon skills. You gain TP mainly through melee strikes, where SS can really use the boost due to its lower base melee skill.
It's arguable that depending on what skill/spells we get in the coming levels 91-99, auto magic skill will become less useful in time. I'd still be reluctant to give up the extra MAB/M.Acc from more magic skill, but if you can get all spells without merits it's not completely unreasonable to consider putting some of those merits in other stuff. We'll see what happens.
You can swap the 5 Auto Melee merits for Repair if you use that a lot like I do but otherwise, that merit layout is the best option for us overall.
I did seriously think about dropping some auto melee merits for repair myself recently, but I didn't do it. Auto melee is just a great merit since it helps every frame.
Two reasons repair is comparatively stronger now though:
1) Get a BLM puppet to 100% HP for Deactivate/Activate. More useful now since even if your puppet dies, you can DEA > Repair and be at 100hp pretty fast.
2) Valoredge tanking (especially with Burts and Cannibal Blade spam). More frequent ability to also use repair improves the potential to tank harder stuff.
Hate swapping to save our auto is pointless with DEA
These days I tend to use it in completely the opposite way to before (Hate dump on to the puppet) just because of DEA. Poor man's Super Jump on a better timer to boot.
Exactly ^^ I also sometimes use it to establish hate on myself. Open with a big automaton nuke, vent onto myself, Stringing Pummel = that mob is stapled to me for a while.
I will say I'm still a little sad that they changed Vent in 2010 to make it no longer a viable instant claim tool as it was for a long time. Now PUP doesn't have any native instant claim abilities. You can /WAR for voke, /DNC for Animated Flourish, but when you're /NIN you don't have an instant JA (best you can do is Ni ninjutsu).
Role Reversal is still useful as an emergency self-cure, and is also nice for situations where the automaton is tanking. Dump your HP onto it, then get cured by a mage (or atma regen).
another quick question for you master Pups. What h2h weapons trial line should i do? what is best for inside aby vs outside aby? is there a difference?
Dustin's reply is completely correct, but I'd like to emphasize just how amazing Burattinaios are. Do what you can to get them, they're way easier to obtain than an Empyrian weapon and they are phenomenal.
In the meantime, yeah Fire Taipan +2 are the standard very solid choice. Ice/Earth/Wind Taipan are situational pieces, but you should certainly prioritize the Fire ones.