The thing about Final Fantasy is that it has always been constantly remaking itself. Your argument could just as easily be applied to VII's Materia system or the way characters in IX are very much locked into their intended role. Removing MP wasn't that big of a change really, especially with the way the magic system works. It's not like you could cast unlimited spells and the summon system was really such a small part of the game mechanics especially later on. I don't think they re-introduced MP because the lack of it was unpopular in FFVIII, but more as a result of their desire to have every Final Fantasy be different from the last.

Once we moved into the Playstation Era every Final Fantasy has been very different in terms of game mechanics and they really never seem to take into account what did and didn't work in the previous games. Some of the concepts have been revisited in different ways in Final Fantasy X such as killable summons and being able to have some extra input in battle. (like Squall's gunblade compared to the interactive overdrives).

The Junction system was never seen again, but then again neither was Materia and I think those were very similar concepts. I don't think there was anything gutsy at all with FFVIII's design. They knew based on the success of VII they could release basically anything so there wasn't exactly going to be that much pressure. But basically when you get down to it I don't think any of the "modern" (FFVII+) games have had that much impact on their successors, and VIII is no exception.