I'm going to steer clear of the debate about whether change is a Good Thing or not, but let's just take stock for a moment. Cricket has gone through various incarnations of the short form of the game including 20, 40, 50 and 60 over competitions and 4, 5, 6 and 8 ball overs. All of these, I'm sure, made sense at the time of dreaming them up.
If the cricket administrators feel that a 100-ball competition is the way forward, why on earth would they arrange it over fifteen 6-ball overs and one 10-ball over? Why not just have ten 10-ball overs? The latest article talking about the idea of replacing bowlers mid-over is clearly drawn from baseball's "bullpen" methodology, which may actually make some sense.
It could be taken further though - if time is the issue, change ends between innings rather than between overs. What about just having a straight 100-ball innings? Bowlers could be changed whenever you want, and they could have a 20 ball maximum which would penalise the team for no-balls and wides.
Basically if you're inventing a new format you might as well be brave and reinvent the whole construct rather than just shoe-horning a "mega-super over" in at the end to make a round number/for dramatic effect.