You still want ports, they actually make networking hardware cheaper overall by moving some of the scaling requirements out of the IP layer and into the transport layer. Imagine needing router which can hold 1,000,000 IPv6<->MAC address bindings just because you have 1,000 clients in your network using new addresses instead of ports! ND code is more complex than the code to bind to ports, but I still like the introduction of ND more than not regardless :).
IPv6 infra will probably never adopt the cert stuff you mention. The protocol is just designed to be able to, it doesn't mandate it. In practice it's almost never done and having everyone do it would likely be harder than getting people off IPv4 has been. On the internet routing side, PKI with BGP doesn't really care about the address format and works fine with IPv4.
For the network manager the 2 biggest changes are 1) All of their client subnets are /64s, no more subnet mask tables. 2) No more NAT, which feeds into the debugging side of things, though some of this is advantage is intentionally lost in a tradeoff for increased privacy via temporary addresses. In the last one it's tempting to tie that back to enormous hardware gains but, in reality, the box at that position of the network needs to statefully track sessions regardless of if it needs to translate them, and that's the majority of the cost.
It's a shame they still have ports in IPv6, but I can see why: imagine having to ARP (IPv6 calls it ND) every connection separately. At least you can just allocate another privacy address if you need more than 65535 concurrent connections to the same destination.
And what is most embarrassing is that truly fully IPV6 capable internet requires less of and lower powered "routers". "routers" will cost single thousands instead of hundred of thousands adn be more capable, speeedier. DDoS mitigations are easier in ipv6 too. And if every customer can have 2^64 IP (or even 2^56) addresses then you do not need "ports" anymore, every service on your server can have their own IP, or even every service customer can have their own ip address how much will that simplify CODE (source of bugs, of latency, of unnecessary payments) and lower energy requirements of login infrastructure ? and debugging ? also just right from bat you can trivially see on upstream router who is initiating DOS... PKI+IPv6 is gift from GODs! If your certificate is not issued for specific ip then "openssl" can drop connection in that instance. Is not that little bit more secure ? faster? less clunky. and with more oversoght for network "manager" ?