Pretty much everyone seems to dislike the popups at the beginning of the turn that tell you to do something and then are displaced with another popup, all in a row and often without allowing you to actually accomplish the things they request. I assume that it's very difficult to fix this interaction if you stay with the same general way of doing things. That is, on each event you would have to suspend the queue notification, and have hooked up 'finished' listeners to all of your potential user actions (spellbook, building, research, etc) that triggers your turn-start game event queue to continue. Especially with how fluid you're trying to make the experience (where you can just click on something else on the main map to jump out of the build queue for a city, for example), that's a big pain. Hint: it still wouldn't be well received even if you got it working as expected right out of the box. The reason is that the user is having control taken away from them.
As it happens, there is a time-honored and straightforward solution to this sort of problem; the turn-start summary. Simply list everything that happened between turns that needs the player's attention, with jump-to links (which can trigger whatever cinematically pleasing experience you'd like). This returns control to the player and completely bypasses the problem we're seeing currently. As an added bonus, the list of turn summaries is a basic and almost free history of the course of the game
Important: be sure to add an obvious way to get back to the list once it's closed.
On an unrelated request, please add the upkeep cost of a city to the city detail tab; since the purpose of some of the buildings is to reduce upkeep, it's relevant. It's also interesting - especially for many strategy gamers.