Now I think the current OOB rules are good enough.
If we complicate the IC-rules, the game will take longer time to play, and this game is long enough that is. Imagine we got a mobilization-wheel like in the advanced counter/hex-games like World In Flames, where a tank takes 4 turns to build, a battleship takes 8 turns to build, and a IC takes 10 turns. It will not be an A&A game anymore.
Besides, when you buy a factory, you are supposed to imagine that the construction of it has been going on for years, and the turn you place it is the turn it is finished, and of course the opponents get surpriced because they didn't know that you had been working on this factory the last years. You might even be surprised yourself as a leader of your nation, because you didnt realize that your engineers had been constructioned this factory before they suddenly one day gave you the kee, man.
While you are quite right to be suspicious of multi-turn builds for units as a general rule, I don't really see how a single rule for ICs would be complicated. It's no harder to grasp than an NO. In fact, whether the rule is 'It takes two turns' or 'you can only upgrade a space by one level' (none -> Minor; Minor -> Major), I don't think that is going to strain the memories of any of our players...
In addition, there are usually only a limited number of IC builds in a game so it wouldn't be a rule that constantly needed to be consulted, but those few IC builds can currently be responsible for massively distorting the game (Norway US IC, etc).
To comment on the justification - how has the IC been being built 'for years', if you only invaded Norway (for instance) last turn?
It's good to be on guard against unnecessary complexity, but I don't think that this either of those - it is justifiable simplicity.