UT1 - based on Earth's rotation only, strictly 86400 seconds per day; length of each second varies; takes a heck of a lot of effort (and time) to measure accurately.
UTC - has same length of a second as TAI, but (for now) tracks UT1 to a precision of +/- 1 second. To achieve that, can have days that are 86399, or 86400, or 86401 seconds long.
None of 3 is planned for scrapping. The only change discussed in TFA is to fix UTC day to 86400 seconds (at cost of letting it drift further away from UT1).
Is it important that midnight is actually midnight? I don't know. I would prefer it to be, but perhaps I can just update my knowledge on when the midnight actually is once or twice a year. Perhaps it isn't a big deal at all. But I wouldn't dare to claim that "surely there can be no problems with it".
And, yes, that kinda means I don't support the leap second removal. It wasn't great, but eventually fixing the software written by incompetent people sounds more like a solution, than breaking the existing solution and making both competent and incompetent people alike eventually come up with a new one (to abolish it as well after 100 more years).
Midnight is almost never at midnight.
Let's talk noon, specifically solar noon, as it is easier to visualize. Solar noon varies throughout the year, and based on the position in the timezone.
Solar noon for two cities in Eastern Time Zone: 11:29:16 - Boston 12:22:36 - Atlanta
Tomorrow, solar noon in Atlanta will be 12:22:50, 14 seconds later than today. No one notices a 14 second shift from one day to the next. As you can see, solar noon is almost never at clock noon, yet no one complains about that. Who would notice a 1 minute shift over 100 years?
The programming problem is made vastly more difficult because the leap seconds are not known in advance. When a new leap second is announced, every dependent system has to be updated.
As the article said, many countries jump forwards and backwards an entire hour twice a year and after the adaptation period we don't notice
We (or our descendants) can try to fix Earth rotation. All is needed is a big enough rotating mass with a variable speed of rotation.
We would use UTC. UT1 would end up only being used by astronomers and whoever else cares about the Earth's rotation.
By the time UTC and UT1 diverge enough to matter, humanity will have either destroyed itself or come up with a new time standard.