Yes, it is basically new game, in terms of development effort. You can't just chop them out and expect the intended progression to remain the same. It would require an end-to-end reworking of unit progression (which has a knock-on effect to design), player strength scaling, AI routines, you name it.Its not a new game, not even close. You already have the engine, the combat mechanics, the units, the Civilizations, etc, etc
Removing Ages is more work than disabling civ switching, but it isnt a new game, not even close
There will likely be engine work required. There will likely be unit work required. There will likely be civilisation work required. I don't know how much, but then again neither do you, so.
Trying to nitpick Siptah's comment (bearing in mind they said "basically", not "exactly") by claiming "well actually, it's not a brand-new game" isn't the strong argument you seem to think it is. It would be a lot of effort. More effort than basically anything else. That's the point.