I think this shouldn't be a dilemma for you, the GM. It should be a dilemma for the players.
If a player can craft a super-secret Alchemy Stone which will single-handedly turn the tide of battle against the forces of evil, then they will want to craft it. However, if it takes two months of intensive work to create, then the forces of evil are still moving against them in the meantime. This causes an interesting issue for the players to solve in-game. Do they take the time to build the super-secret Alchemy Stone? Do the forces of evil know that they are attempting this and try to stop them? Perhaps that would be an interesting session idea; the one character is trying to craft the MacGuffin, while the others defend his efforts from the adversary.
If it's less plot-related or dramatic crafting (like just a decent potion or other "nice-to-haves" for the characters), then you can consider simply allowing the following understanding: every night before bed, the character spends an hour performing whatever their craft is. You don't have to play this out every time. Then, after an agreed upon number of in-game days, they get whatever their trinket is. Even this is somewhat of a stretch, though, since for most crafts it would take at least an hour just to set up their equipment properly.
With that said, this is the very reason that crafting skills generally don't mix very well with an adventuring party if you're attempting to be realistic about the time frames. That's why every fantasy video game simply glosses over the crafting with a blacksmithing sound ("clang-clang-clang") and perhaps a very short timer. The amount of effort it takes simply to smith a sword is enormous, never mind whatever complex things your PCs are likely attempting. So you can either compromise your realism slightly in order to maintain the fun of the game, or you can let it be an interesting in-game dilemma.
To address the specific issue mentioned in the comments below: If you want your Wizard to be able to scribe spells into his spellbook faster but don't want to directly manipulate the rules-as-written (RAW), let them go on a quest for a magic quill which allows faster scribing or something. This would be a (hopefully) interesting in-game solution to a problem that the characters face.
You seem to be looking for an out-of-game, sort of meta-game solution to what is ultimately an in-game problem. And it's in-game problems which make games interesting. No amount of meta-game shenanigans will change the fact that in the real world it takes a week to simply forge a sword, so you will need to either bend reality, change the rules, or trust your players to handle it. For me personally as a GM, I would never force my Wizard to spend an entire day putting a new spell in his spellbook, because it's my opinion that the RAW are not the most important thing. My job as a GM is to remove obstacles that are in the way of everyone having fun.
Let me borrow a common answer from StackOverflow, usually applied to software development:
- Premature optimization is the root of all evil.
- First measure, then fix.
First, Measure
There are many elements in Pathfinder that take time, especially for an unexperienced group, but attempting to address all of them before the first session of play is probably not cost-effective. You might spend several hours readjusting the character sheet layouts, when the basic layout wasn't a bottleneck to begin with.
Talk to the players and try to establish the first session as a test-run. Like a tutorial-stage in a video game. Start with an ultra-short adventure or encounter that features the main game elements (combat, of course, but some spell casting and skill checks) to make sure you've got full coverage, and run it to see what takes time, what breaks down, and what goes smoothly. This will give you the information you need to tweak properly, to see what really needs help.
Then Fix
That said, there are several elements I've run into myself with Pathfinder games, especially with new players, that will probably pop up in your measurements. Here is what we did:
Pre-calculate common rolls.
The character sheet has convenient fields for the attack/damage totals. USE THEM. Many players leave those blank, but they add a couple of seconds to every combat round. Calculate as many common scenarios as you can and add them to the sheet. Adding +2 when flanking is easy, but if you write your total attack bonus in one column, and your total-while-flanking in another, it saves you a second of calculation.
Are you a ranger with bonuses against a favored enemy? Note it down explicitly, rather than having to recalculate. And always keep them up to date when leveling up. To employ software terminology again, a lookup in a table is cheaper than recalculating every time, even for a simple calculation.
Use spell shortcuts
Most melee attacks mechanics are relatively straightforward, but when it comes to spells, each one is a bit different, with their own rules and conditions. Checking out a spell's description after you cast it can bring the combat to a screeching halt, especially if you only have one book that has to be handed around.
There are two good solutions I've used, depending on the player.
- For myself, I use the Pathfinder Spellbook app for my Android phone. It let me collect all my available spells into one list (I usually play spontaneous casters) for super-quick lookup, without leafing through a book. There are more apps with more data, but this one was specific and streamlined.
- For another player, who preferred paper to screens, I used one of the adaptations of 4th Edition's Power Cards to Pathfinder. In 4e the number of powers and their specific description are given even more prominence, for martial as well as arcane characters, and so the basic character sheet has large, easy to read cards for each power with its numbers, parameters and descriptions. There are several community-made solutions for Pathfinder. I used Perram's Spellbook, but there are others. They used to be linked to from the PFSRD, but I can't find them there anymore. Google "pathfinder power card" for options.
Delegate
Your players might be new to the system, but they can still be given general tasks to take pressure off of you. The classic one is intiative - have a player be in charge of tracking initiative for everyone in combat, and call out the next character or enemy in order. This isn't hard for a player to track, doesn't really require system mastery (just have everyone give that player their initiative totals at the beginning), and can take a lot of pressure off of you.
Best Answer
Empowering a prophecy without railroading, using mechanics, is very much possible. The "stick" is not so useful here as is luring the player with the "carrot". There are a number of more-or-less successful games that do this with great success*, to the point that some use it as a central part of character development, so there's evidence in the wild that this is possible.
Substantial bribes
All the games I've observed doing this effectively offer a significant "bribe" that tempts players to choose to act in line with their fate. Such a bribe must be large enough to give the player a true dilemma – do I act with freedom to choose the "best" course of action for my character, or do I take the big mechanical boost and do what the prophecy says I must?
The bribe has to be big, unbalancing almost, in order to make it large enough to be the equal to how much a player values their freedom of choice. The extra that they're getting must be valuable enough to really make them consider it. In D&D terms, a +5 or more to all skill and hit rolls for the duration of the time where they are facing the direct consequences of their choice (the resulting battle, the escape from the crypt, etc.) might be suitable. Another effective carrot is the game's improvement currency: a large XP bonus (perhaps 10%, or more, of what they need to level) can be very tempting for a player.
This can be tweaked as you go, to. You don't have to tell them at the outset that every such moment is worth 1000 XP — instead, when they come to a pivotal moment in their fate, you can mark it as such by saying "…and if you choose X against your better judgement, it's worth N experience." You can offer variable carrots tailored to the importance of the choice, too, so that you give bigger bribes to properly balance the sides of the dilemma.
Free choice
It must always be a free choice. You might set the dilemma, but a player hugely values their freedom to choose.
By putting the choice into your player's hands, you make it more likely that they will fulfill parts of the prophecy/curse/fate and you don't railroad it. As long as you're always prepared to accept the player's true choice (don't up the bribe after they refuse, for example), they will feel it really is their free choice, and you'll get much more buy-in for when they do choose to accept the prophecy.
Not everyone likes talking mechanics
The one caveat is that some players who go for deep immersion will really dislike baldly discussing mechanics when they're trying to choose according to their character. There's no real good way around this without seriously annoying the player and undermining their buy-in. The compromise application of this idea is to not tell them that they have the choice – but when they do choose the path of prophecy, narrate how their sword swings truer (as you start appling a hit bonus to their rolls) or how a great weight of foreboding settles in their chest (as you give them bonus XP as an aside). This will create the association between bonuses and accepting their fate, without interrupting their internal narration and breaking their suspension of disbelief.
* One example is The Riddle of Steel. When you're acting in line with your Fate during a pivotal moment in the prophecy, you get a very large bonus to all your rolls during the fallout of the choice. Another is Dungeon World, where you can get into situations where if you do a thing that you normally wouldn't choose, you get to mark XP.