Banjo-Tooie

At its best, Banjo-Tooie is a far better game than Banjo-Kazooie, with only Click Clock Wood eclipsing the best moments of Tooie. At its worst, Banjo-Tooie is just awful.

The main new mechanic of the game is splitting up Banjo and Kazooie. I thought this was dumb as shit to start, because the two could barely do anything apart. Once I got all the moves, however, I started to appreciate the new puzzles.
Without Banjo, Kazooie is much lighter and can move faster and fly further. Without Kazooie, Banjo can use his backpack to carry things, hide in, and more.
The problem is that Banjo has to be told by Jamjars that he can put things in his backpack. It's annoying that you have a puzzle where you need the taxi pack in the third level, but you arbitrarily can't get that ability until the fifth, for example. The original Banjo-Kazooie did a much better job with this, giving you all but one ability as soon as you needed it.

One of my favourite puzzles in the game is also plagued by this. In Witchyworld, you can get burgers and fries from concession stands, but you can't take them out of the park. There are cavemen in Terrydactyl Land who are starving, and the only food in the game is in Witchyworld. There is, however, one secret path out of Witchyworld, which leads straight to Terrydactyl Land. Unfortunately, you need the claw clamber boots, which you need to wait to get, since they're in Grunty Industries. It's annoying and arbitrary. (you can actually skip this by entering from the Terrydactyl Land side and then dying, which will warp you right to the entrance, but that's not intended)

Grunty Industries is one of the best levels in this game, but I absolutely hated it the first time I got there. It's a confusing labyrinth that you need to learn front-to-back. There are two systems in place to help you move quickly between the floors of the factory, but only one can be used at a time. Normally, you use the warp pads to go to each floor. When Humba Wumba turns Banjo into a washing machine, however, he can no longer use the warp pads, and must use the elevator. You've really got to learn the factory's layout in order to succeed here.

The worst level in the game, by far, is Jolly Roger Lagoon. I thought I was going to love this level the first time I got there. The pirate town aesthetic was top-notch, and the idea of collecting doubloons to trade for goods and services was something I really wanted to do. Unfortunately, the pirate town is just a small part of the level, and the meat of the level is godawful.
The two N64 Banjo games have awful swimming controls. Kazooie softened this by making there be no enemies underwater. Tooie decides that Kazooie was far too reasonable, and adds underwater combat to the barely-improved swimming. Jolly Roger Lagoon is mostly a water level, and features the new horrible underwater combat heavily. I was absolutely pissed.

Another thing I hated in this game was the new minjo enemies. In both Kazooie and Tooie, a game-spanning objective was to rescue the jinjoes. They'll yell and whistle for your help, and then you pick them up and it's all good. Minjoes yell and whistle for your help, then they'll attack you. If you kill them, they respawn, and continue to annoyingly yell and whistle at you.

In Kazooie, the main antagonist, Grunty, would always talk to you in rhyme. It was her most memorable and defining trait, hearing her constant rhyming taunting in the overworld. Tooie introduces Grunty's sisters, who force her to stop rhyming. The writers completely removed the most memorable trait of their villain, and it seems incredibly lazy, regardless of their intention. Imagine if a Paper Mario [ペーパーマリオ] game made Bowser mute. People would be up in arms. oh wait