1) lights, both front for vision and IMPORTANTLY bright rear strobes for being seen and waking up drivers, and all being very long-lasting
2) bearings - crank, wheel, pedal, and I'd say most importantly headset. Notched headset bearings long past now. Front-end wobble too. Hours spent cleaning and adjusting crank and wheel and headset bearings now long gone. A truly teensy bit of additional resistance in sealed bearings has been a worthwhile price to pay. Yes, there was beauty to a really smooth Campy or Shimano wheel bearing, but the lower maintenance is also worth that connoisseur's loss.
3) handling - I had some great SLX and similar bikes, but none ever matched the handling that I've had on several carbon bikes of the past 20 years. There is nothing like being able to throw yourself into a fast descent with a bike that is totally secure and really wants to hold whatever line you choose. Front-end wobble was way too common on old bikes, as was poorer handling. Obviously some of the older bikes did handle very well, but overall the average good bike from back then did not handle as well as recent good bikes.
4) di2 electronic shifting is a big improvement - never missing front or rear shifts, much lower maintenance (like cable replacements and adjusting and things like frayed and breaking cables), and with the Ultegra version at only a modestly higher price
5) tires - more durable choices now
6) clipless pedals - yes, they're nice.

One really questionable "improvement" that holds a significant safety risk: very low spoke-count wheels. Yes, they're lighter. BUT. When a spoke broke one time for no good reason on a Dura-Ace rear wheel while I was just cruising along on a country road my rear wheel almost completely froze, and I barely saved that moment from a bad crash. At the wrong time, with so few spokes, a broken spoke can mean disaster. With a 36 or 32 or maybe even 28 spoke wheel no such severe threat is involved at all.