Bear in mind that I love 3e. It is such a vast improvement over 2e and 1e that words can't describe it. I no longer have headaches from trying to DM. Still . . .
The 3e poison system is pretty bad. Poison is useless. The game designers went from overly-lethal 2e poison to useless 3e poison. Poison does too little damage and it takes too much time to do have what little effect that it does. To top it all off, whomever conjured up the poison costs was out of his mind. Why does rat poison cost most of a year's income (and it likely won't even kill a 3e rat.) Delay Poison makes it useless to even ATTEMPT to poison a PC or an important NPC.
The CR system SUCKS. It is AWFUL. It takes too much time to calculate and it is too subjective. I would love to see what formula was used to assign CR to certain creatures because I don't believe there is one. I think someone took a dart board and threw darts to determine CRs in the Monster Manual.
I love the skills system with two exceptions:
1. DCs are too low for certain tasks, and there are too many fixed DC. There are a number of skills where all you really need are a certain number of ranks because there is nothing with a higher DC. 20 is also too low a DC for a difficult task. At high level, many skills become irrelevant because the DCs are so low.
2. The ease of making skill items wrecks the skill system. In order to be able to make a skill item, the maker should be required to actually HAVE that skill and there should be a max rating that you can give the item unless you are an epic level character. Some items in later products specify this, most don't.
I also like the way that 3e codified how to make magic items. They didn't go far enough though and some of the codifications are illogical:
1. Craft Rod is a stupid category. This is a relic of 2e. All of the rods can be farmed out into Craft Arms and Armor (Rod of Lordly Might, Rod of Flailing etc.), Craft Staff (Rod of Thunder and Lightning, Rod of Metal and Mineral Detection etc.- Just Give them charges again), or Craft Wondrous (Rod of Spleandor etc.) The Rod category has too many dissimilar items that are in the same grouping only because someone reclasified them as "rods".
2. Craft Wondrous needs to be broken down into several feats. As it stands right now it is the Uberfeat. There are too many items in this category that could form cohesive categories of their own and deserve their own feats. For example: Craft Magical Clothing (all Cloaks, Capes, Vestments, Shirts, Boots, Belts etc.) Why is it all of the related magical clothing was not entitled to their own feat but the heterogenous rods category did merit its own? Also: Build Wondrous Architecture. This should be its own feat as well.
3. Forge Ring: Why just rings? Why is it if it's shaped like a small band that goes on a finger it is a ring, but if it is a bigger band that goes around the head it is a headband that is made with the Craft Wondrous feat? Rename this feat as Craft Magical Jewelry and include (Rings, Earrings, Brooches, Clasps, Phylacteries, Scarabs, Amulets etc.)
Lastly, there are a number of spells that I have gripes about:
Delay Poison, Haste, Heal, Harm, Mass Heal, Mass Haste (in my campaign these spells do not allow you to cast a second spell in a round), Greater Magic Weapon (lasts WAY too long), all of the Shadow Magic spells (these have been busted since 1e but no one ever fixes them), and Teleport (nix the unlimited range. I created an "Extra Long Range" category of 5 miles per level. This stops the PCs from trying to teleport to the moon or Scry onto other continents) are just some of them. Timestop is the great granddaddy of busted spells. This one has been debated to death on these lists before so I won't bring it up again.
Tzarevitch