I will admit I am sad to see them go, I don't like the Bethesda mindset of "that didn't work out quite right so lets just scrap it instead of tweak and fixing it." This has been an ongoing trend with them for some time now.
Arguments for removing them seem to be mosty focused on these factors:
- They were tier based anyways, so it just makes more sense. How about instead of keeping them tier based we made them actually function like an RPG and they provide you a skill check - meaning your lower skill may actually allow you to get by that high level lock (or what have you) assuming a good role. You can then factor luck into that as well to modify the results. Many mods did this for previous games, it was a common trend to add the weight back into the Skills and SPECIAL.
- They resulted in a "jack of all trades" character. Well, this can be corrected by actually taking some consideration to how many Skill Points are granted to the player. If you reduce the amount then you can end up with characters not being this "jack of all trades" defacto type. You get strengths and weaknesses based on your choices. The main reason for pumping you so many points to begin with, I suspect anyways, was that the Skills were tier based and thus you needed more points to make an impact. Using fix one has already removed that as an issue so every single point makes some impact on success.
- It makes more sense for them to be perks as it is less confusing. I fail to see how Skills being your core and Perks being special effects that added personal flair to your character was such a convoluted system to understand. Perks have historically been something completely different from Skills in all Fallout games, and so this really doesn't make things less confusing when you approach it.
Of course I feel like a minority in the community, as the general public is more interested in Action Adventure games than they are in RPGs. Again, the historical split here has been the level of complexity. Action Adventure has been hack-and-slash or FPS with some RPG bits tacked on to keep a simple and oriented form of gameplay. RPGs have been geared towards the complex interactions of different systems that you can manipulate.
I think the frustrations expressed by some of the community come down to that simple facet really. Bethesda got their name from making great RPGs, but now they are focused on making Action Adventure games. This shift is disconcerting when it bleeds into historically RPG lines like Fallout or The Elder Scroll, more so when Bethesda now has multiple liscenses under their belt that go across multiple genres. I don't want my RPGs to become Action Adventure games, use a different line or make a new one for that. On the same token, don't do thinks like make Wolfenstein or Doom into something they are not (which it does not seem as though they have really, to be fair). Can you evolve the games, sure, but you don't need to take away from their core to do it. I love some of the new things they have done with Fallout, and some of the Fallout 4 features look amazing as well, but it doesn't change what I see in this trend.