I have to agree with mariocerame, don't worry about wonders cloning each other too much. I mean, in the real world there are wonders and buildings that bring similar benefits, why not maintain some of that in Civ?
For example lets use the Theatre of Dionysus which was a copy of the Globe Theater. Why change it? We also have the UN and the Apostolic Palace which are very similar. Its ok to have more then one globe theater, especially on large maps! In fact, I'd prefer that bonus over +2 artists. I also think it would be great if there was a copy of the Great Pyramids, why should only one civilization have it's benefit?
As for the Armor Factory, I liked having to build it so I could produce tanks. It almost simulates industrialism as only productive cities will be able to build a factory to build these tanks, you don't always see small AI nations with hundreds of tanks running around. It was A GREAT BALANCE MECHANISM. I think you should keep it for that very reason. Perhaps you should first build an airport before you can build aircraft (at least better aircraft) or a harbor/drydock (better ships).
You can make primitive units without these buildings but to build higher tech and improved units then you need to build a harbor, drydock, airport, and armor factory. See what I mean?