Both Ramirez fights can use Destruction, and the chances of him using it are random like other enemies, but he's more inclined to use Destruction if you use buffing abilities of any kind (Power up, Speed up, Regeneration, etc).
I tried fighting Ramirez 2 several times (Which is kinda boring going through all of it time after time) and sometimes he used it once, sometimes he used it more consistenly. In fact one time he kicked my ass using it three times in a row, which NEVER happened to me in years upon years of playing this game.
About the items, it was one of the things I couldn't find a balance I wanted. Your idea is similar of what I wanted at first, which was to nerf the Ilchymixes (as they're the easier ones to obtain), but I never ended up doing it. I think to make Ilchymixes healing only HP or MP, and leaving both Urala and Polly's specials being the same as they take more effort. But first I need to see if those changes would work as intended, as sometimes you could get unwanted results.
Again, great job with the patch.
P.S. If you haven't done this already, I recommend going through a full run of the game with the latest patch. I'm sure a bunch of little things have changed since you last played a full game, and it would be wise to try to see how it all comes together (especially the new Alpha Storm and new Lambda Burst).
EDIT: Is it possible to change what crew members can do? I ask because Merida is kinda useless.
Oh yeah, I've been thinking about giving it a complete go in it's actual state.
But I need some time for it though, and I'm rather short of it lately. Not only real life matters, but also I'm about to finish two other things I've been messing with that have being eating most of my free time, and I'm quite anxious to finish and rest from Rom Hacking for a while (I love it but it takes too much time, worst part being test-playing everything). I want to release those and go hide under a rock and forget about everything for some time, if that makes any sense. I haven't touched a game that wasn't hacking/play-testing for months.
But definitely it's on my mind and once I get to it, probably make a final version ironing out any little thing that I see (Although of course that's if I see something to be improved).
The thing with Merida is that it is a mechanic that ended being unused. At one point in development you could buy and sell ships (Which, in all honesty, could have been really, really cool to me) but we ended with two story-driven ships, so the value of the ship is, as you said, kinda useless. I thought she was needed for a Swashbuckler Rating but it seems I was making that up in my mind...
I don't know if the game will like changing Merida's effect, I never tried. Maybe give her the same ability that Pow has, and let the player have the character they like the most would be the best option, as giving her one effect from the other characters slots would break the choice-making idea of the crew member system. I'll have to look.
But again, I need to test it first, because I don't know how the game would respond.
And, as always, thanks for your feedback. By the way, Happy new year!
EDIT: Okay, here we go:https://www.dropbox.com/s/miis0yn7yx735zr/SOAL%20Maeson%20mod%201-49.rar?dl=0
Ilchymix now recovers all the MP from the party, and only MP. You can only use it outside of battle like before. This way the dishes made by Polly and Urala will be more useful, and no longer made pointless by Ilchymixes.
Merida now gives a passive bonus of 15 to the Quick to the ship, instead of increasing the value which did nothing. She now has something worth to offer.
Descriptions for both things were also updated too. The hack's page is being updated.
Edit 2: I updated the hack again, because of a small oversight. You can download it again by using the same Dropbox link, or wait for the hack's page to be updated to 1.49a.