The SP system is great, but seems a little buggy. Sometimes my characters will stop being able to rank up even though they aren't at level 8 yet. I know there's the guy in the Highwind that resets it to level 1 or 4 for everyone, but it can end up making some characters overpowered if I'm not keeping track of ranks on my own. Additionally, as someone else mentioned, it would be really nice to be able to see the current ranks of each party member other than when they go up. It would also be nice to see when I SP and if possible how much. In the earlier versions, it looks like there was a message at the top of the screen when you got SP, but that appears to be removed. Most normal enemies don't really seem to give SP, but it's hard to tell if I'm wasting my time or not trying to grind for it, other than in the crater. One last thing that would be very convenient, though potentially very difficult, is to allow characters to reallocate their stats. Even if it's only allowed on disc 3 to avoid balance issues, it would be a very nice feature. Many characters have their usefulness in certain areas change depending on what equipment and materia is available at the time. My Red XIII is completely useless because I never really knew what to do with him, but now that I'm at the end of the game and have to use him for his sidequest, it'd be nice to be able to patch him up just a bit. I can reset his rank to 1 (along with everyone else) and just add on to him that way, but it feels kinda cheap. Also, for rank 6 and 7, it showed up as 16/8 and 17/8 for multiple characters. Seems to be just a visual bug, but it's there.
Carmine and Viridian are both significantly easier than in the base game. Each has around a quarter of the max HP, so Carmine can be easily defeated in well under the time limit, and Viridian is always damageable and goes down pretty quickly as well. I'm not sure if they were intended to be this easy, maybe you're meant to fight them as soon as they become available? If this is the case, I was fooled. Given the increase in difficulty and all the extra superbosses added, I assumed that these two fights would be enormously difficult. But, I ended up easily overpowering them when I finally got the courage to fight them.
Balance overall is very good, I never felt like I needed to grind at all in the main part of the game, and each boss provided a fun challenge that could be overcome with some smart thinking. Whether it's good or bad, it's worth pointing out that the weakness system of this game really prioritizes Earth and Lightning spells, since most bosses are big and some are also robots. This also makes Kjata severely overpowered early on, and is likely one of the first methods to do 9999 on bosses -- however, I feel that summons are appropriately balanced so even having an easy 10k by the end of disc 1 isn't gamebreaking, but still might be worth tweaking. Fire and Ice both were extremely underused for me, most of the time bosses were not weak to them, or were also weak to either Earth or Lightning. The same goes even more so for Holy and Water, which I didn't have until I got Planet (didn't really do Enemy Skill). I basically had all my bases covered with just two magic materia, occasionally using poison-all for fights against multiple humans. So, I think more variety in weaknesses would be good. Also, it's pretty unfortunate that Sense stops working, because it would be nice to be able to see the weaknesses for endgame fights, but I know that can't be fixed.
The fight with the second Jenova form was almost a welcome difficulty spike, if it weren't for the cutscene. I liked the idea of zombifying my team members one by one, and it was a very challenging and rewarding fight. However, while I was doing the fight, it was mostly just infuriating, because every time I lost I would have to watch the "famous" cutscene in it's entirety. The boss for Cloud's sidequest had a great solution to this, where after losing you can go into the menu and change your loadout before fighting again without the cutscene. If that could be implemented in the Jenova fight as well, it would help it immensely.
One more issue with balance is the stardust item. It can be reliably farmed starting at Midgar raid, and you get a few before that too. It's a free 24k on basically anything. Even without W-Item, it potentially trivializes the rest of the game if you let it. Especially thwarted by it are the KOTR guardians, who each have very low HP but take very little damage to compensate. However, 2 stardusts is nearly enough to kill each of them, and 3 is more than enough. This means that one of the hardest bosses (in my opinion) guarding the most powerful summon can be beaten in 2 rounds by any party tough enough to survive a few hits. With W-Item, it's an objectively superior alternative to 4x-Cut or Quadra Magic (except Ultima), by doing 48k non-elemental in a turn. W-Magic + Quadra Magic is potentially better, but has pretty high costs unless you also make sure to have MP Absorb, and you may need MP Turbo to reliably exceed 48k. Aside from the fact that Quadra Magic + MP Absorb locks the game against a few enemies, like Carmine and Pinnacle Seph, it also takes up quite a few materia slots that stardust doesn't need. The only deterrent to doing this is the time it takes to gather stardusts (with the hopeful assumption of not abusing the W-Item glitch), which isn't really that long once you have the Conformer, and is still the path of least resistance for beating a lot of the harder bosses in the game. I went out of my way to avoid abusing the item after realizing its power, but I imagine that if you go all in, you can really ruin all of disc 3 for yourself.
Some glitches: having anyone that's not Cloud as the leader tends to have some weird effects, though mostly minor. I never really used Tifa so I can only say for Cid. The jumping animation on the field (used a lot in the crater) tends to cause an additional animation which takes like 2 seconds. It's not much on it's own but it makes navigating the crater with Cid very annoying. Also, generally when walking into a room where the current leader is supposed to be staged as an NPC, you will spawn at the NPC location rather than the entrance you walked in from. I mentioned this in my previous post with the highwind, but it's happened to me in a few other places as well. In a similar vein, during the escape from Junon, the last cutscene before you get to the airport allowed me to use the PHS, and I could freely move anyone in and out of my party. This allowed me to make a team without Cloud, Tifa, or Cid, meaning I could run around with Red XIII for example. Changing screens too much seemed to crash the game, and at that point I was more interested in playing the game so I didn't play around with it further. I'm sure there's some interesting things that could happen because of that.
A minor bug/oversight is that for some characters, their canon names and given names show up inconsistently for their innate ability messages. For example, I named Vincent "Raven" in my game, and the message said something along the lines of "Raven's Innate Ability: Vincent will regain HP". For Cid, it was switched and had Cid in the header, and his given name in the body. Doesn't really affect anything, but it was just something I noticed that made me do a double take.
Goldberry seems to do some weird stuff, and I'm not sure if I just don't understand it or if it's not working properly. From what I understand, it prevents you from blocking status effect with e.g. ribbon (and possibly resist? but I didn't have it at this point). However, often I would be unable to heal from these status effects too. I would need to use multiple remedies and dispels in order to recover from the effects, but I could never tell how many. I have a feeling that status effects are possibly stacking. For example, normally if you are poisoned, another attempt to poison you will fail; if the Goldberry is somehow bypassing that check, it may possibly poison you multiple times, and hence would take multiple tries to heal. This is just a guess, and I didn't test it too rigorously because I was pretty frustrated at the fight. Also, they will not kill you if you don't attack them. If you have the game on wait, and they get you into a situation where you can't attack (say, by Stop-ing your whole party), then fight never end. I waited for about 20 minutes watching them walk around to see if the petrify counters would ever go down or if stop would go away, and neither of those things happen. It was kind of funny and a little annoying, but once you know that happens you can just reset right away. And speaking of Resist, I'm unable to pair it with all; it only casts single target, while Esuna targets all. I feel like this may be an intentional balance decision, but I wasn't sure about it.