I wonder sometimes if we aren't thinking outside the box enough. For example, I think weapons should each occupy their own skill and be filled with perks that are level locked. Roll all damage into attributes and skill level. Perks should be reserved for unique effects that will greatly impact if not outright change how combat is engaged in. Or maybe I should say perks should be effects or alterations that open up more options (I liked an example above about axes, I think Dargor wrote about it... like the new avatar btw). I think we would just have to accept the fact that talent trees might be more sparse in terms of our skills, but I would really, REALLY like to see attributes make a return. And I would kind of like to see them handle them like they did in Fallout 4.
Make them static, make them dictate certain player parameters, and fill them with their own perks. A lot of boosts can be thrown in here (health, stamina, magicka, resistances, etc.) along with some interesting stuff. It would be interesting to have a main quest specific perk tree as well, assuming we end up being the chosen one from some prophecy. I always thought Skyrim would have been vastly improved with a dragonborn tree that we used dragon souls on to unlock more perks.
Finally, if there would be only one thing I would advocate for, it would be crafting skills being side quest driven. I still believe we should have to use the skill and "pay our dues", but we should never spend a hard earned skill point on a crafting skill. Our crafting skills should be improved by seeking out trainers and completing tasks for them to prove our proficiency and move us up to the next tier. I want the game world to feel more vibrant and alive and I think increasing our interaction with it is a great positive step. Additionally, it always seems like trying to time a bad event when it comes to selecting a crafting perk. On the one hand, you gain access to more powerful potions, armor, and weapons, but on the other, it is usually difficult to craft a completely new set of gear if you are ahead of the curve. If you fall behind, it is often the case that the gear you can craft is no longer worth the effort and so you are just flushing points to get to the endgame goodies. Furthermore, every point put into a crafting skill tends to be a point that could have gone to a more directly survival oriented perk.
I think a lot of the woes of using perk points for crafting stemmed from the options present in Skyrim and the balancing of when things were available, so I think they could do a much better job given the chance, but I'd prefer to not have crafting skills using any perk points.
Did you play Dragon Age Inquisition? The crafting system in that game separated style and material a little bit like what you are talking about. So I could get a schematic for a sword and then choose the material I wanted it to be made out of. In that game the materials were distributed into tiers and then higher tier materials allowed the weapon to do more damage AND different materials led to different colorations. Eventually they added a transmog-esque system for their crafting so you could get creative with color schemes and looks (and so you wouldn't look like a clown).
Granted, I think what you are talking about is different, but I just brought up DA:I because for those of us that played it, that crafting system where you got to choose your material also lost its appeal pretty quickly. I would definitely prefer a game where material did not so heavily impact usefulness of a weapon or piece of armor. Even in a fantasy universe, with rare exception, gear shouldn't be such a deciding factor. I think ultimately aesthetic choice should also impact how a player chooses to outfit him/herself. Having said that, I do think DA:I showcased how useful modularity would be to a crafting system (even Fable 3 showed this to an extent). So, if I could choose the blade of my sword and the material for that, then the hilt of my sword and the material for that, and possibly the leather wrapping for my hilt and the material for that; THAT gives me a lot of choice and simple palette swaps can showcase the change in materials with small increases in performance (and durabilty if they decide to try and bring that back).
Whatever they do, they need to get their ducks in a row where smithing is concerned for the next game. There were all kinds of items that were unimprovable (and thus practically useless for a smith) for no reason and I thought the smithing tree was an uninspired mess (but hopefully if they take my advice on crafting above, we won't have that issue in the future). Ultimately, they just need more. Crafting systems are great but they are practically useless if you only have a few things to change. Take FO4 for example. There really wasn't a whole lot to switch up. Most guns had auto and semi-auto receivers, a few stock options, and then a selection of standardized scopes. And that was it. I know the art team probably has a stressful job, but they need to keep hiring people and just crank out assets that can be tweaked to give a broader selection or, again, make everything modular and just leverage the exponential growth in combinations as a way to keep things interesting. I'm rattling on, exhausted, but I had to get this thought off my head. Hopefully it makes sense.