For our team, newer was definitely better in terms of a stadium. But, I think if you look at not just the Niners new stadium, but a whole lot of NFL, NHL, MLB and NBA teams, the move into more expensive and glitzier digs was not 100% good for teams. A lot of them gave up traits that made them very tough places for opponents to visit and win in.
For me Exhibit A: Yankees Stadium. Probably the most storied venue ever in the history of pro sports and the new place just has no soul compared to the old. Old Yankees stadium had a nasty, almost scary vibe. You could feel the weight of history there. You looked at right field and thought, "Wow, Babe Ruth stood there. At first, Lou Gehrig. Center, Mickey Mantle." etc, etc, The new one... it could be anywhere really.