I like the honorifics. Sure it's a localization, but it's still taking place in Japan and I think it adds a nice little touch to the game. No hate for those who do not prefer it though. It's not to everyone's taste.
Well... since it's in Japan, it just would sound weird if it suddenly disappeared. Blah blah... localization and a few of the honorifics are questionable. If you want to get rid of everything like honorifics, we might as well change Chie to Carley and make her black. --- Canon is only meant for blowing stuff up.
The issue is that they're difficult to translate, and without them, you lose some meaning towards relationships present in the Japanese version.
Sometimes you can throw in equivalents, like changing a -kun prefix into referring to the character with a cutesy nickname. Doesn't always work, though, so I understand the translator's dilemma. --- "There'd come a time when life'd pull us apart. S'not a reason to avoid people."