Good list. Let me add to it:
a) No significant cleanup of the bases classes in terms of flexibility and space covering, quickly leading to 3.5's unending proliferation of classes, prestige classes, and unplaytested class power combinations all over again (or even worse).
b) No significant improvement in the big holes in the 3.X skill system - spot vs. hide, diplomacy, vague professions or vaguely defined skill areas, etc. leading to no real improvement in handling commonly encountered cases.
c) Encounters that tend to play out in very formulaic ways. Ei, everyone uses thier per encounter powers in the same sequences every combat.
d) Gamist per encounter concepts, for example, mundane classes that mysteriously can only perform a particular manuever once per encounter even though they have the physical resources to perform an equally strenous but different maneuver in the next round. Encounter beginings and endings that are vaguely and arbitarily defined under the rules.
e) Lots and lots of actions that are passively triggered and so must be maintained in memory at all times to run encounter smoothly/correctly (this is IMO worse/harder to run than lots of choices for actively choosen abilities).
f) Reduced player choice. For example, Wizards that cannot be built as necromancers, summoners, enchanters, etc. without new base classes, new talent trees, prestige classes, etc.
g) Design bandaids by which I mean root problems are ignored in favor of patching up the system in some other area. For example, per encounter resources slapped on as solution to 15 minute adventuring day.
h) Scope reduction as a system solution, by which I mean problimatic or difficult features of the system are simply removed because fixing them seems too difficult. For example, 'save or condition' is problimatic because it bypasses ablative hitpoints, so the option are simply removed rather than the system fixed. Or for example, overly narrow skills which are rarely used are simply removed leading to situations where either its not clear what skill applies or else character suddenly is found to be unexpectedly proficient in seemingly unrelated skill. For example, removing a little used profession skill resulting in all characters with wilderness lore being experts in handling sailing vessels, or all tightrope walkers also being expert kayakers, etc. Problimatic spells (divinations, shape changing) solved by thier removal.
i) Balance achieved through cosmetic variaty. That is, all classes are fundamentally identical spellcasters with common arrays of abilities that in practice differ only slightly outside of the classes fluff. For example, a fighter with the per encounter ability 'long strike', 'knockdown' and 'power attack' and a wizard with the per encounter abilities 'energy blast', 'telekinetic push', and 'arcane blow' where the various abilities are fundamentally interchangable except for thier flavor. Alternately, everyone explicitly plays a spellcaster in some form, resulting in a Wuxia world were anyone who is anyone can 'fly'.
j) Loss of genericness. Flavor so intimately tied to game mechanics that a particular game world is virtually assumed by the text and conversion to different assumptions are difficult.
k) Christmas tree/multiple overlapping transient buffs/effects back in new clothes with little or no net gain to justify the disruption.
l) Rapid acscension to 'epic' levels of power assumed by the game system.
m) Demonic/diabolic themes pushed as fundamental to game play.
