My view on what is bad:
Too modern a perspective.
Like news that is touted like TV or newspapers rather then town criers.
Magic is no longer magic. It is just black box technology that you can go down to your local and buy off the shelf. How much
good fantasy literature has the adventurers going down to the local market and buying all the items they want. It
is a staple in sci-fi to go out and buy the best or go to a black market to do so, but normally magic is treated as something special and not like a slushy at the local 7-11.
This is part and parcel with the powergaming design paradigm that the creators are pushing. Just go and read about the most optimised character builds. For instance where mithral chainmail was a reward to an elven hero by an elven clan and only rarely given to outsiders for exceptional circumstances it is now characterised as the optimum buy for a nightshirt. The current official site is catering for lowest common denominator power gaming hack in slash, nothing wrong with that, just wish there was a higher fibre content for other gaming blends for us oldies

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This easy access to special items diminishes the wow ohmygawd factor. All items short of artifacts can be gathered at will. Players optimise their characters, often using spreadsheets with look up tables of feat and item combos. To make sure they can get into a prestige class...nice ironic title for something that isn't so prestigous because everyone and their dog can have one, no offense intended to werewolves.

... they will also spend more time predesigning the optimum path for their character. Its not special if everyone can do it. The value in diamonds is not because they are shiny, it is because they are rare.
It leads to situations where players spend far more time designing the characters and tinkering with them then actually using them in combat let alone the meagre portion left over for a half nod to role-playing.
Having said the bad, now for the good.
Note that I said perspective. The attitude may be sub-par but the core mechanics have improved.
The skill system, BAB and the way AC is handled vs the older systems such as THAC0 show that the mechanics have improved vastly. It makes it easier to learn and allows more exceptions to be added... and the way most exceptions to the base rules are handled are as feats... a very very neat solution IMDHO
I wouldn't mind seeing the current skill system to be extrapolated one stage further... that it covers and includes combat. You have a BAB based on skill points and it can be a cross-class skill. Of course with BAB at present when compared to skills it is a three tier system full points, 2/3rd points and halfpoints... I wouldn't change that so much as make the skill system have 3 tiers of skills. Full points... every point you spend gets you a skill rank, 2/3rds points every point you spend you get 2/3rds of a skill rank, 1/2 being the current cross-skill.
Just using the current system it would mean that you could start with a BAB of 4 as a fighter... so an offset might be needed, or not depending on how people feel about level 3 fighters having multiple attacks (beyond using two weapons, one weapon and shield, cleave ...)