The "mishmash of stuff" is one thing that really stood out to me about Star Wars: Dark Forces IV: Jedi Knight III: Jedi Academy. I haven't played the Jedi Outcast campaign since it first came out, and I only vaguely remember the storyline, though I do remember very vividly a lot of the gameplay moments that have really stuck in my head for being completely amazing. I've never played a Star Wars game with a story that really moved me or did anything for me for that matter, and Outcast wasn't an exception.
I think Academy's mission select idea was one of the very few steps that game took in the right direction. Its biggest problem was it came out a very short time after Outcast and had very little of anything new or different to offer.
It felt like an expansion pack that was being sold as a complete game.