I really like the the rarity system. I don't read it as a form of banning any more so than the fireball spell is "banned" because it's only available to casters who are level 5 or higher.
It can help manage player and GM expectations, getting everyone on the same page with regards what spells, items etc. they might be able to find. Thus players can avoid putting together character builds who's effectiveness is entirely dependant on getting a specific magical item or spell.
Gating spells etc. can help limit unexpected actions that circumvent a scenario (I'm actually ok with players doing this). More importantly it presents an opportunity to make obtaining uncommon spells etc. a more significant part of the adventure. So rather than regarding teleportation as a circumvention of a scenario, making obtaining it a possible solution.
I think it might also help encourage players to get a little more invested in the setting which is always a good thing.