Yes that button glitch is one I have seen, I am still trying to work out exactly what is wrong, but chances are there is some over spill of a couple of pixels that cause it, it also happens with one of the robot icons.
With the BOS, chances are you are playing the random map where they lucked out with loads of gold at their start location (I think it was gold) So they get a huge lead, this is all just temporary map stuff, eventually we will find a way to fix the random map generator and also create proper fallout maps.
City Capture is not a bug, in order to capture cities you have to research 'Conquest' this then allows the main units to capture cities. The purpose of this is to prevent rush crushing of factions in the beginning of the game, as some factions will be stronger in the start than others, and when the fallout maps are complete they will also start much closer together. The early game is all about raiding, pillaging and slaving each other, pillaging is actually a very necessary part of the economy for some civs, particularly raiders, and it boosts all things, not just gold. Again this will come into play much stronger when the Fallout maps are added as you will find it much easier to reach each other without being eaten!
The upgrade times for improvements is intentional for two reasons:
1) When you research the right technologies your workers can build the upgrade version for a price, so if you have the resources you can 'Force Upgrade' your improvements and economy.
2) Certain civics boost upgrade times for improvements, so if you have a corporate government for example, they will increase the investment and speed of development of your improvement infrastructure. This all still needs to be tweaked and balanced between the many factors to get it to play just right.
right now what little energy i have is going on trying to deal with this main CTD bug, but the solution continues to dodge me...