You may be missing my point. It isn't possible to have every possible combination as a seamless connection, at least not unless there is limited options (eg the no interlining airline example I referred to above).

I also get annoyed when some connections are horrible (I have one coming up on same airline which switched from easy morning connection to a horrid middle of the night arrival and wait several hours with terminal shut until my onward flight). However, I still prefer the enormous flexibility that alliances offer compared to not having so many options.