I really love the effort put into this so far. This is a fun Mega Man X title to attempt. I've run through the main 8 stages a few time before running it in full, which I've done twice now, both 1.00.1 and 1.00.3, Rookie and Hunter mode. I do like many of the adjustments made, especially within the Vulpine and Axolotl stages.
The removal of lava in the final drop in Vulpine was much appreciated, although I think some of the culprits too are the spikes on the horizontal moving walls. The health drop to clue the hidden wall to the capsule is a solid move. (Could do something similar in Snapper Stage where the heart container is. I found that out of sheer luck!) What I'd like to see differently is better patterns of the floating platforms, and maybe adding platforms or adjusting them in the vertical climb section with the spike walls (maybe add in non-spiked gaps on the walls instead of all spikes), just before the heart tank. Granted, the boot upgrades would make it an easier climb, except you can't get them without the Flame weapon used later in the train stage. I choose to go to this Vulpine stage first because I found it a decent route to collect everything without backtracking. Vulpine is also a pretty easy first boss to go for, and a fun fight. I'd like to imagine for all stages being able to speed through them. Although I'm not a speed-runner, it is nice to have levels that you can ingrain into muscle memory and go through them in a breeze. This stage has a lot of directions: up, down, left, right, and all the hazards to navigate over and around. The placement of platforms ought to add to forward mobility and momentum rather than a barrier, especially since this is Mega Man X, where fans play for the wall dashing maneuvers.
For Axolotl stage, I think the platforms added at the bottom of the initial dive aren't necessary. They don't add anything in my opinion. I do appreciate the couple removal of spike floors. I think another commenter mentioned the camera positioning, which is what my thought was. I don't know the mechanics of programming that, but when you've dropped down to the beginning of the spike sections, I think it's better to have the camera show the entire floor than try to show partially both the spike ceiling and the moveable space (also would help in Vulpine Stage for the descending platforming-over-lava section). Since I've dropped down I already know there are spikes above me so I know not to jump up, but I have no idea about navigating what's below me. Even from memory it's not reliable, especially when it's still a work-in-progress. Finally for this stage, I wonder if the area for the heart piece is too spikey, or at least too narrow to be reasonably consistent. The only best option is to take intentional damage from the submarine mines before dropping through. But then the escape out is dicey. I feel like it ought to be hazardous to get to - to make the reward more rewarding - but without trying to punish you afterwards. This is like X2's Hunter Stage 3 difficulty level and beyond. For a casual player it should be a little more tame. Ramp up the difficulty in the final stages of the game.
A little afterthought of the previous two, I wonder if relocating the Capsules or swapping what armor you get from them would help running of levels (of course this means needing enough disks if placing it earlier in the stage. That's the drawback of having the disk requirement). For instance, you get the air-dash boots at the very end of Axolotl stage, where having them throughout would be helpful to navigate the narrower horizontal spike sections. Also, on the topic of armor parts, I'm not convinced on the visual difference once getting the quick shot upgrade. Either the regular lemons could be nerfed before getting the upgrade or the upgrade be buffed more, because both damage and speed feel roughly the same.
In the Space Stage? (Primate), it runs pretty well. I like the ride armor mechanic. I noticed though in this newer version an addition of the exploding platforms, particularly towards the end. One at the end of the ride armor section and another right before the boss door. Both of those seemed out of place.
I think there was another spider added in Snapper stage, which is cool..... Insta-death though? Even most mini-bosses (which I noticed you don't have any) don't dish out insta-deaths. Those are the closest things in any stage that resemble a mini-boss, and I guess they have spiky legs, but insta-death?
I've seen other people say they don't care for the disk collection mechanic. I actually like it! It gives you things to search for. I think though when you are trying to speed through the levels on a 100% run, placement is key. For example, there's a spot in the Desert stage where one disk is barricaded behind a rock wall that you have to break through. It's timely and feels like a let down to only get one thing out of there. How about adding a health drop or an Extra Life along with the disk? I don't think you need to move the heart container there, I think that's fine where it's at, and no need to duplicate the same type of requirement to get an item like you already did the Capsule. Otherwise for one disk, remove the barrier. In another stage, Tundra stage, there is one I always miss because I hop in the ride armor and forget to go down the cliff to grab it. Several of the levels, like this one, have you go down these little cliffs to grab disks, and there are so many to check that it gets to the point you forget exactly which ones do and do not have anything. Also in Tundra stage, I noticed when trying to get the heart container, I could not do the boot jump after jumping out of the ride armor. I thought I could before. Normally I'd go down there without the armor and use the boots and fist move up, but I thought I could too out of the armor. I also like being able to jump out of the armor easier (being able to dash out is the biggest plus) but I wonder if it got overcorrected, because it's a little too easy, and sometimes I jump out midair when I don't intend to. It might be me though. (I paused right here and hopped on Mega Man X and played through Chill Penguin to the ride armor section. Input for getting out is up + jump, regardless of in midair or sitting on the ground). It just seemed like I was hopping out of the floating armor too easily compared with the previous version 1.00.1. Getting in the armor immediately after getting out also is either delayed or the hitbox is too small. I think the latter.
There is a lot of slow animation entering any type of door (checkpoint and boss). It is a bit of a momentum killer.
The input timing for Hadouken doesn't feel as smooth as OG Mega Man X, or I'm misunderstanding the actual input and it's altered from the original. It's not as consistent to execute.
I do like that E Sub-tanks don't deplete entirely when you use one because of wastefulness, however, I'd much rather they fill my entire health bar. I'm low on health in a tough fight and the full Sub-tank only refills the quantity of health the tank is holding. The tanks refill unusually quick, which tells me they don't hold a full maxed out health bar worth. In X-X3, a full Sub-tank refills you to 100% full, while partial Sub-tanks refills a percentage.
Some weapons could get revamped or have more utility. In the case of Flame, it "fires" off too slow, in my opinion. Although it's Snapper's weakness, the timing, proximity, and hit box you need to target him are not skewed towards your favor. The charged version works pretty well, but the normal shot animation spreads from behind slowly and usually too late to hit.
Finally, I think, both Vile and Sigma don't seem to have a clear weakness, or maybe that's by design. In X1 Sigma was weak to Spark, and then in X2 weak to boomerangs (first phases). Regardless if going for 100% and using Hadouken on him (which I eventually had to do on my second playthrough) it's nice to have options. If he did have a weakness, then it was minimal at best, not clearly damaging. Give players multiple options for defeating every boss, or at least an easier option for the beginner players. In particular, a weapon that works against Sigma's movement and fighting patterns.
Overall, great game! I enjoy running through it and look forward to updates!