Actually it's just book one (like the actual first third/fourth of GOTM, since the novel is split into "books") that's hard to get into. It never flowed for me, but once I powered through that it was just an easy read and got to Book 2 (Which I think is the one that begins with the introduction of Kruppe) it was more engrossing. In book one there are so many different plot threads being introduced that it's hard to grasp anything. Although to an extent that still applies to the entire book There were a couple parts that could be clarified by a re read, like the part with the Jaghut tyrant heading towards D-stan.
And yeah, I've heard the Malazan crew (Chris and Naren and I can't remember who else) mention that the first book is the least impressive (and most confusing, since it introduces a lot of the concepts and characters and shit) by far, and some shit about it originally being intended for a screen play. Definitely good stuff though, if this is the least good one it definitely bodes well for the quality of the other nine books.