Named branches don't really exist in git: there's only a moving target name that refers to a leaf node. This means there's no "history" associated to a branch except for the parent commits. But in merge commits with several parents all parents are considered equal, and the system does not contain info about which commit belonged to the "main branch" and which was imported in. This information can be valuable in some cases. This leads to a lot of rebasing just to keep the commit log clean, but this actually rewrites history and destroys information.
Also, there's no support for keeping two parallel views of the same repository (for example, an internal view with lots of subcommits, and a cleaner public view with more detailed messages, and perhaps fewer privacy-compromising names/timestamps).
Finally, handling merge conflicts is still a PITA, especially on LaTeX documents.