I don't think this has been considered in the first place, when the HQ and normal factories were introduced.
The effect of the mass extractors will be that ecoing will be easier. That changes the game progress. It also determines the way to get T3 mass extractors. Always start with a T1, and upgrade. At the moment there is the option to ctrl-k the T2 mass extractor, reclaim the wreck and build a T3 one. I don't think removing this choice is such a big deal but it's a choice that would be removed nonetheless.
If you make this upgrade chain make sense, and make the T3 mex more expensive to compensate, you'd be changing the dynamic of the late game, where mass extractors get destroyed and you want to rebuild T3 mexes. This is more expensive, so if you lose a section of your base, rebuilding is going to be harder.
I don't think the effect will be that big on intel structures. You won't have many, especially as you go for omni sensors. One per player is usually enough. Most times one per team will do (although it's a bit of an issue if the omni gets sniped).
As for the shields, the Cybran already have this, but they are more expensive. The total cost of an ED5 is 4260 mass. A UEF T3 Shield generator is 3000, Aeon is 2400. Seraphim is 3600. The balance of Cybran shield generator costs is a different one though. Each upgrade gives you an instant new shield bubble.
I started off thinking "yeah consistency is better" but after this small wall of text I'm not so sure anymore