I haven't used meld for a long time; the website says its three-way merge is still in development, while kdiff3 has had that for more than twenty years and it's (for me) the main reason I use it. The three-pane display with the merge result in a fourth pane at the bottom is just so easy to use. (The second reason I use it is that it allows you to mark lines that should align with each other.)
As I wrote I rarely use the GUI tool for conflict resolution because I am most of the time just fine with diff3 textual format in my editor. So I have no experience which tool would be best. I used kdiff3 15 years ago (mostly pre-git) and have drifted over to meld over the years. The reason for that has been lost in history, not sure whether it would stay that way if I started to systematically compare them today.
Meld certainly does allow to manually align lines. But sometimes I have struggled when doing several alignments in a single diff. Not sure whether kdiff3 would do better or it's just user error.
Where meld certainly fails is huge files. Its performance can be horrible. But that affects generated files like logs, not source you would have in git.
