During movement and battle resolution phase there are a lot of popup windows from diplomatic and political actions. Quite often they block the view on the map e.g. when you get an interception, so it is hard to get the picture of the particular situation and difficult to decide whether to make the interception and how much of your force to commit.
Nevertheless, these popups give some interesting information, so I would not want to disable them completely. But it would be nice to have the option to postpone them to the phase after turn resolution (Events phase I think).
Alternatively you might generally collect them in the message log, so the player can have a look at them again,when he feels the need, even after he click away the initial popup. This could already be one step of what I requested in a separate thread: Summary of the previous turn