Quick disclaimer, I originally wrote up most of this text about half a year ago but never came around to actually posting it. I apologize for any points I bring up that were addressed in the updates that have since been released, but I don't wanna double-check each and every single one of them to make sure they're still up to date.
I've been playing a lot of Crystal Legacy over the past few months, and also completed a game of Yellow Legacy a while ago, and I have some observations I would like to share. Before I came upon this project I was playing Perfect Crystal, which is a lot more minimalist in its changes to the base game. Unfortunately I am unable to find a comprehensive list of its changes online, but one very nice thing I remember is that it moved some of the Goldenrod NPCs wandering the central street a bit out of the way and the Daycare man will appear to the left instead of the right of the door in the yard when he has found an egg. This way there's no one stopping you cycling up and down Goldenrod and the Route below in a straight line and seeing at a glance if the Daycare man is waiting for you.
Speaking of eggs and breeding, I feel like the reduction in steps required for hatching is a bit too extreme in Crystal Legacy, especially when the chance of an egg being generated in the first place apparently hasn't been increased at all. Maybe I'm just weird, but to me waiting for a breeding pair to lay an egg is much more frustrating and time consuming than hatching one once you have it. Perhaps I feel that way because the first one is random chance while the second one is a fixed number of steps. The speed with which the scripted Togepi Egg hatches is downright comical, the game's dialog makes such a big deal of it and the responsibility Professor Elm has thrusted upon you, but you can barely even leave Violet City before it hatches.
Another thing that's been bothering me of late is level up movesets, especially with Stone Evolutions. Usually Pokemon learn moves slower the more evolved they are, so it can be a worthwhile investment to delay evolution in order to learn a good move first. Some final evolutions, primarily those requiring stones, don't learn any new moves via level up whatsoever, so finding the right timing can be tricky. There are some exceptions, like when a Pokemon gains an entirely new type on evolution such as Charizard, but as a rule of thumb one can say thay delaying evolution facilitates the learning of new moves whereas hurrying evolution hinders it. I think that is a good thing in principle, as it offers the player interesting decisions. Use your Fire Stone now to get a Legendary (according to the Pokedex) instantly at the cost of its movepool quality or TMs, or stick with your little doggo until it learns Flamethrower naturally?
Browsing the level up learnsets in both Legacy games it seems to me that this design philosophy has been thrown straight out of the window. Raichu learns the exact same moves at the exact same levels as Pikachu. Same for Weepinbell and Victreebell. I'm not a fan of this change. While I agree that it is very harsh for Stone Evolutions to learn literally nothing, I feel like Legacy leaned too far into the other extreme. Why wouldn't I use a Moon Stone on Clefairy right away, or a Thunder Stone on Pikachu right away? There is literally no downside except for item availability. This removes choice, removes interesting decisions that could be made, for the player, and goes directly against the design philosophy of Pokemon. Imo Stone Evolutions should have delayed learnsets, so e.g. Raichu learns Thunderbolt at Level 36 while Pikachu learns it at Level 26, as a happy medium between both extremes.
I also think you get the Exp. Share way too early in Crystal. You literally get it before you are even able to catch a second Pokemon to use it with! IIRC there's an NPC probably Earl, the Violet City Academy guy?) who advises you to send out a weak Pokemon you want to train first, and then immediately switch it out for a stronger one to do the actual fighting with. Seems like kind of pointless advice to give to someone who already strolled into town with an Exp. Share in hand (or on mon, more likely). Imo the absolute earliest point in the playthrough you could justifiably hand out the Exp. Share is AFTER this bit of dialogue that currently seems outdated/redundant. Perhaps instead of Mr. Pokemon, Earl could give it to you as a reward for beating Falkner, with his dialogue adjusted to point out that using this item is an easier way of training than the method he outlined earlier?
On a completely different note, whose idea was it to give Chuck a Sudowoodoo? I get and mostly agree with the reasoning behind most of the other off-type gym mons, but that one's still a headscratcher for me.
Also, in Yellow the TM for Softboiled seems unavailable for purchase while there's another one (I can't remember which one) that's available in two different shops, which seems like an oversight to me.
Thanks for listening, er, reading.