Kaubel instructed you not to make lists like this.
Zones and Quests
I enjoyed leveling in BC. Pre BC, the questing system didn't really give you very good rewards (remember every item having spirit on it?). In Burning Crusade, there was a clear progression and just about every quest would give you an upgrade. Plus, there were way more than enough quests for each zone. You could sort of pick and choose where you wanted to go. In vanilla wow, it was more or less - go to the Barrens, then eventually STV, etc. The quests in general were more conducive to leveling as well. There were less of those stupid delivery quests that made you run all the way across the zone.
Daily quests were great. It gave every class, no matter what spec or professions, a way to generate income.
I liked how the dungeons in general were shorter than the vanilla wow dungeons. Taking 2 hours to complete an instance is too long in my opinion, they should take 45 minutes, tops. I'd rather not get into the heroic badge gear debate because that degrades into Casual vs Hardcore. But I will say that from a raid leaders perspective, it's much nicer knowing that no matter what raiding experience an applicant had, they at least are going to have some T6 quality gear from heroic badges.
Heroic dungeons and later the Daily Heroic quest made every dungeon worth revisiting and somewhat entertaining.
I like how they expanded on the tokens for T6 system. I hope they stay with 3 set tokens per boss kill model. I enjoyed Black Temple and I enjoyed Sunwell Plateau. I hated Serpentshrine Cavern - the trash often felt harder than the bosses themselves. I think we can already see from wrath that they've learned that making entry level 25 man raids too difficult is a bad thing.
Another thing Blizzard needs to remember is that the loot from raids needs to be good. When BC was first released, SSC gear was often worse than blues from questing. This has long since been resolved, but as arena gear keeps getting better and better, they're treading on a thin line.
I don't think anyone thought the way they distributed Atiesh was a bad thing - why did blizzard go back to a RNG system for legendaries? Bad move. So frustrating for me personally when my guild killed Illidan 50 times since we first started doing BT and never got a mainhand warglaive, when one of the bottom of the barrel guilds on my server has two complete sets after killing Illidan 6 times.
Sunwell was great except for the stacking of Shaman. This has been pretty well documented in other threads, no need to QQ more.
I loved arena, but I hated druids. Arena was the main reason why I even bought the expansion in the first place. It was great until Druids started to dominate 2v2 and 3v3. Then it felt more to me like a battle to find the better druid partner. Most of the problems with S3 and S4 I think could have been solved simply by more players queing up (or just removing the Druid class from the game)- but once everyone got their rating they wanted they just played their 10 games a week and dodged any decent teams. Sadly, I don't think they'll ever get class balance perfect. Case and point - the last 3v3 tournaments before 3.0 was released were all won by Warrior Warlock Druid - and most of the finals matches were straight up mirrors.
Battlegrounds were just the same as vanilla wow. Making honor a currency used to buy pvp gear was obviously a great improvement over the High Warlord system. However, I hate the matchmaking system. It doesn't reward you for playing as a team, since the games take longer to pop up and you'll only play against another team - meaning less honor per hour than just solo queing. People resorted to using third party addons that cleverly made every player individually que at the same time to circumvent the matchmaking system. Even when I qued by myself, since my gear is better than the average player I'd wait in a long que, only to get into a game that's already started with 3 horde versus 15 alliance.
Giving every profession something unique to that profession only as well as giving them access to raid quality loot was a very good idea. It made professions actually matter.
On the other hand, Sunwell was so very well tuned that DPS had to be more or less perfect. With items like Drums of Battle in existence, it made it virtually a requirement for any decent guild to have everyone be leatherworking. The same can be said for when SSC and TK were new. Alchemy stacking was ridiculous - Flask, 4 different kind of elixir, food buffs, etc. Making more professions give you something useful for raid buffs is a good thing - but keep it in check. They need to be careful not to make one particular profession SO good that everyone MUST have it, like Tailoring pre-T6 content or Leatherworking once Sunwell was released.
Mana. Mana was stupid in Burning Crusade. It got to the point where there was no point at all in keeping track of it in PVE, every class would never run out of it. This just led to dumb stuff like ignoring the intellect and MP5 stats, grabbing all the haste you can get your hands on and then just chain mana potting to compensate.
Best and Worst
Best: 5v5 Arena and Sunwell, in my opinion.
Worst: RNG (Mace Stun, Imp Hamstring, Windfury Totem, Frostbite, Resists, Etc), Shamans in PVE, Druids in PVP
Why exactly did Blizzard choose to throw so much raidwide damage at us in Sunwell again? Was it because they wanted to give other healing classes an edge over paladins? I think that was the reason. Paladins were the top healers when BC was first released. Seeing as they're homogenizing everything for wrath - I don't see why they shouldn't give every healing class a strong single target heal and a strong group heal option.