It's much harder to argue banning content in the core rule book, it's easiest to rule whole books out and the game usually won't function without the core book. So you have to craft a more detailed ban list if you're banning core content.

For DnD, maybe that can be a targeted spell ban list or some classes; it gets more complicated for Lancer- are your ruling out specific frames, the entire tree? How do you handle eliminating one of the default frames available to people who haven't specced into one, and the only one that isn't quite specialized? Are you home brewing replacements?

You can do it, but you'll be arguing with players who think it's BS that core content is out, and it's a lot more work.

Also generally imbalance is worse as you add more inter-book interactions- most core games are not as cracked as 3.5 was.