Some thoughts on the level changes on 1.00.3:
I like changes in the Vulpine, Squirrel and Axolotl levels, although i think you didn't need to completely remove the mett on that first jump on vulpine's level, maybe just moving it a little further beyond the vertical line traced by the right wall on the top would have been enough.
I do think, however, that maybe you overcorrected a little on the Axolotl level with the bridge of crumbling platforms at the start (i think the cable's destruction animation gave you enough time to see the fish enemies on the water, maybe placing the cable a little further down so you see 2 fish would do the trick) and the Primate level with those first 2 two jumps with the countdown blocks guiding towards the wall opposite of where the enemy is... until they don't. On their own, maybe the new guiding blocs are defeating the challenge too much? but then the guiding the blocks also give you a false sense of safety and predictability because then on the 3rd jump the gap now leads you straight into one of the 2 enemies, so earlier the challenge was consistent and you at least learn the lesson if you failed the first jump, but with this change, initially, there's no challenge, then the level trolls you.
On the Squirrel level things get more interesting. So what I see is that you signal the wrong way by blocking it with destructible blocks, if you go in the direction of the block, you're punished with an offscreen enemy. This is more the case in the new layout, in the older one this is true for the first fall, but for the next you fall into an enemy either way. It's definitely an improvement, however, the choice of making the wrong direction be blocked by destructibles is a little weird in my eyes. In the Mega Man series the convention is that the path that requires more work, more upgrades, weapons, etc. is the one that contains a reward for your effort and skill, so, according to this historic convention that is present in many other games, the player is psychologically enticed to go down the direction of where the destructible blocks are, which sends them into the enemy traps.
As you may notice, my issues are with consistency and intuitiveness
In general, to me, the problem with the blind jumps and the offscreen enemies or instakills at the end of a fall are most of the time more of an issue of the things being visible in the screen before you jump (or early reactable with the tools you're expected to have at that point) and of consistency on what to expect when jumping down things, rather than an issue of instakills and enemy placement on themseves. When you fall into a platform, the camera doesn't follow X until his sprite is centered, it stays a little above his sprite, leaving more screen space above than below (naturally, the opposite is true for climbing), and this results in the player not seeing an enemy, platform, bottomless pit or spike floor by just a little. This is how the camera behaves in the snes games, no problem with that, but the thing the snes games did most of the time with the level design and the enemy placement is to layout the things in such a way that the platform you need to jump to, the threats, the traps and the enemies would be readily visible, at least partially, from the platform the level is hinting you to make the jump from and with the camera dragging behind. The games breadcrumb you into your next move. Also, when the only way forward was jumping down a long fall, you knew that you were going to be safe by staying close to the wall. The games would typically reserve more hardcore jumps for the fortress stages when the developers could expect you to have your air dashes and whatnot, while keeping reaction times more viable for no armor on the regular levels. Right now, i find some inconsistencies on what's the right guess on jumps of the same type in this game.
Obviously, the classic games weren't perfect and sometimes they pulled these troll moments, but my point is that there's more potential for improvement on adjusting the visibility of the obstacles and the consistency of the traps rather than eliminating them altogether.
Regarding Vulpine's level, I really like the health drop hinting you towards the capsule, very clever. The downwards dissapearing block section, now that i think about it after 3 playthroughs, is not so bad. However, even on my 2nd or 3rd attempt in my first playthrough I didn't feel positive of where the second dissapearing block was when i made the jump, and i believe it's because the rails they're on blend a little too much with the background, and with the anxiousness of the situation I didn't registered it. I also believe I didn't guide myself by the rails because the rails tell me there's a platform at that X coordinate, but i don't know if the one spawning next is going to be on that rail. I believe there needs to be more contrast between the background and the rails where the blocks are and the blocks that are just barely below the camera need to be visible from the one above them. You already do this with the last 2 floors, you can see the next block's position from the one you're standing on, so maybe the solution can be to place the blocks above the out-of-sight ones a bit lower, just enough to see the next one.
Yes, the smart strategy here is to just slide down slowly, that is the exploratory casual approach and it's very good that the level design allows for a casual, paced down walkthrough. However, the greatness of the Mega Man level design lies on the skill layering: working for multiple legacy skill levels of playstyles so that on your first playthrough you can walk around and slowly slide down walls but you can also dash around and trust on your reaction skills as a veteran MMX player.
Again, this is just my take, I don't hold the absolute truth on the solutions. Thank you for your time if you actually read this.