The materia bonus/penalties were altered recently to have more of an impact, but there's likely fine-tuning needed to be made.
Yeah, I noticed. I started playing through 7th heaven and then updated the .exe and realised they had changed (luckily I was just in sector 5). I think independent and summon materia are OK, it was the rest that I thought did not fit that well (at least to me). Magic materia is now less harsher while command and support had some important reductions. Yet again, it may be the best option to avoid using the same strategies through the entire game.
EXP was an issue in the original builds of the game, so I built in some 'soft-caps' to every 10 levels (11, 21, 31, 41, etc.) to try and help with that, increasing the EXP given by enemies in later areas at an exponential rate to boost players through the caps; it sort of works, but not for everyone. A potential alternate solution is maybe setting it so that enemies give reduced EXP once the player party is higher level than them.
As you said, it could work for some people. That would be nice if you're trying to 'semi-force' people to play on certain levels in order to maintain the challenge. However, if you were trying to keep underleveled, it would still be the same problem. Maybe there could be an item/option that prevents you from gaining exp at all? Anyway, don't worry too much about that. The exp system is fine for the average player as it is right now .
As for Destruct, I think it starts equipped on Red XIII. If Sample HO512 made use of some grand ability that gives statuses like Peerless or Shield, then some text claiming Destruct/Debarrier will work against it, then that might keep it in player's minds as something that can turn a fight around for the future. I've seen a lot of runs where Destruct is usually shelved and forgotten about.
That's a great idea.
I'll probably start a second playthrough sooner than I expected as I got some days off. If I find any bugs or problems within Arranged Mode I'll be sure to post any feedback that you may find useful.
Edit: One important thing that I forgot to mention is that the new E. Skill 'Transfusion' is unobtainable from the Death Joker enemies in the North Crater. They seem to be impossible to manipulate (there is no 'miss', as if they were inmune).