Regarding the edit: Those problems are made up imho. Merging questions could be managed similar to tags. If a question is inappropriate for one site and you wanted to delete it, an option to select which site is not too complicated. Up-voting affects the user on one specific site. The ID could be something new or just from any of the selected sites (plus e.g.: if that one is removed, the question gets a new ID from the next site). Why connect and not do the giant site for everything? Well, I don't know how bad the situation on SO is, but connecting sites for some questions is different.

You are giving a nice example for what is said here. And to peek into the discussion there, I can see two problems: 1. There will always be some users lacking the experience hence being in need to ask general questions 2. There are problems (as Pavel indicated) that can be solved by different means. Some time I tried to ask something purposely general such that I might be redirected. Don't get me wrong I tried to do my homework but couldn't narrow it down. -> Did not get an helpful answer and the question was deleted. Great Help.

@Pavel I guess that were a more higher ranked user ability. Else people could spam slightly related communities to get more attention.

How about a feature for posting just the same question and answers to several communities ? I mean that every community sees the very same question.