I've played EoS a little with your randomizer, and had quite a bit of fun. I had a few issues with the difficulty, so I'll go into detail about that.
1. The very start of the game is way too hard. It isn't uncommon to get one-shot or two-shot by the first enemy. There's nothing the player can do, because they have no items at this point.
How to fix: add an option for "easy Beach Cave" in the randomizer. This would lower the levels of the Pokemon that appear in Beach Cave, which should help this issue a little. Or maybe it would choose Pokemon with weak starting movepools(might be a bit harder to code) to place in Beach Cave instead.
That being said, it really isn't that big of a problem. After a few runs, you should be able to make it through by sheer luck, unless you get incredibly powerful enemies.
2. Later in the game, it becomes way too easy. This a combination of factors:
a) Gummis spawn a lot more than usual. Each gummi gives at least a +1 to your stats, which makes a huge difference once you collect a few pages of them. The enemies do not gain power at the same rate that you do.
How to fix: Let the user adjust item weight, rather than making it totally random. This way, the user can choose how easy/hard they want the game to be.
b) The player gets a lot more money than usual. They can sell TMs they can't use, as well as Gold Ribbons(and similar items), to gain huge amounts of money. This means that they can buy Revivers from the shop every day, becoming pretty much unkillable after buying enough of them.
How to fix: Again, let the player adjust item weight. They can choose to make TMs spawn more/less frequently to change the difficulty. Another way you could do it is if you adjusted the selling prices of items so you don't get a huge return on gummis, TMs, scarves, and such items.
c) The later enemies are sometimes weak. In the normal games, endgame is full of dragons and other threats(Dragonbreath Onix, Discharge Porygon, etc.). Obviously, in a randomizer, they're going to be completely random. But, it would be nice if they were a bit tougher than the enemies at the start of the game, and not just in level.
How to fix: Give the user the option to weight the encounters so that the ones with good movesets and typings appear more frequently toward the end. It might be a bit tricky to program that, but the end result would be great, I think. Or, you could let the user adjust the level curve a little. Even Tackle turns into a scary move when being used by a high-level Pokemon.
3. The player frequently gets access to broken moves. Spore, Sweet Kiss, Imprison, Smokescreen, and so on just completely get rid of the difficulty. The battles change into one-way beatdowns instead of an exchange.
How to fix: Give the player the option to reduce the frequency that stun moves appear.
I don't know if you're still developing this tool, but if you pursued some of these options, I feel like it would really improve the program. If you do decide to do any of these, please keep them optional, because I don't think that every user will appreciate these changes if forced.
Also, I should note that I haven't managed to get past the starting menu with text randomization. It just crashes on me.
