Removing cutscene skipping allowed new players interested in it to enjoy that portion of the story without having to do it on their own unsynched. Aside from Gaius' voiceover, I really can't say that's a wrong thing. And queueing in these two specific dungeons is a choice you make - nobody is forcing anything to people doing the roulette. Allowing people to skip cutscenes would revert it back to the start, where people were basically cut out of the fights (something I personally loathe, I'm here to kill stuff gods darn it!) and left behind probably fending on their own because they have no clue where to go next. As a story-heavy dungeon, this would make it horrible.
...except it still is, due to loading times difference and everyone knowing where to go except for new ones who have to sprint between cutscenes to keep up with the rest. Which brings me to my stance on this: delete Praetorium and Castrum Meridianum. Now - this might sound like a radical approach, and it is, but it's because this dungeon just can't work the way it is. There's a lot of Nero/Cid story in it, not to mention Gaius, and they still are relevant in later expansions! But at the same time it's long, extremely long and the cutscenes all over make it horrible. I really, really hope that this is in the list of the MSQ rework. Castrum could be turned in a duty call with less walking forward and back and fighting reused garlean magitek bosses and more meaningful action packed in it. Turn Ultima into a last quest Trial (similarly to Thordan, Shinryu and Hades) and Praetorium...well I was going to suggest turning that into a duty too, but then we'd miss the last level dungeon leading into the trial so - I guess it would be a dungeon with a true bossfight with Gaius at the end. With a better voice acting, please, listening back to those cutscenes I wanted to bite my own ears off.