The disapointing thing I thought was in the train station, 30 minutes in, where you're going to see Tenenbaum. There's a map of the train line, with each of the stations marked, and just like that, you know where you're going, and what each level will be, right up to the end of the game.
Kind of killed the suspense. If you've played Half-Life, there's a bit in there where you're crawling through a pipe. The pipe breaks and you suddenly slide down it, through a false ceiling and end up in an office storeroom. It's a memorable moment, and one that signals an unexpected move from one area to another, each with its own style, and using the train in this manner leaves no scope for this kind of shift.
It felt... full of gaming sugar. While it's great fun firing bees at people, and setting them on fire, and punching them with the drill there weren't the visceral shifts of the original; no origins becoming clear. BS1 had some meat to it. Whether it's down to its sequel status or... I don't know. I didn't find myself thinking "this is like Deus Ex!" so much either
And frankly, the 'find damsel & save her plot' was getting a bit tired when Mario did it. Although admittedly not many fairy tale princesses look like the Big Sister...
Apparently the development process was a bit tortured, with massive swathes of plot and setting being created and discarded. That may account for the structure and plot being a bit lumpen; maybe someone enforced a simpler plot on it to keep development time down, and get the thing out the door in time.