I'm glad they changed that bridge dome. It made the proportions of the ship seem odd.
Getting rid of those silly spikes on the nacelle domes and shrinking the deflector dish were also improvements.
Part of MJ's genius when designing the Enterprise
was the "Hornblower effect" -- evoking subtle impressions of an 18th-century sailing vessel on a spacecraft from hundreds of years in the future.
With a bit of imagination, the warp nacelles atop those tall, slender pylons suggest masts and sails. The briefing room's angled bulkheads and curved beams are reminiscent of an old ship's cabin. And why the elevated outer ring of work stations on the bridge? Partly to create visual interest, but also as an excuse to put a railing there.
And then there's the obvious.