Some humble suggestions:
One of the most unspoken things that I think everyone knows since X4 came out, and needs to be addressed, is the fact that every time you die your weapon energy gets refilled thus making energy balls useless, and killing off a huge thing in the mega man series, I've never once remembered ever needing a energy ball in the PSX series, or thinking of them as a lifesaver. This is a flaw that needs to be fixed, and is made even worse when you get the armor piece that makes weapon energy consumption less
. Not only should you make weapon energy consume more energy like in the first X game ,but upon re spawn you keep the current amount of energy, making the game feel more risky and making your game play choices more serious. In case you DO need energy in emergency or extremely difficult cases you place some energy balls along the way. Also if on Xtreme you remove the game over checkpoints, like in the SNES games, where when you get a game over it returns you to the stage selection screen, instead of staying in the same level, with the option to save. This modification will surely make this hack a must-download for ALL mega man gamers.
Also there are two levels that could be improved upon, those being Dark Dizzy's stage and Tidal Whales. The problem being with Dark Dizzy is that the first segment of the level alternates between being slow on purpose to being normal, which honestly feels like lag, and if you could instead try something else like making the stage more like Spark Mandrills stage from X1.
Tidal Whale seems like you've already tried something, although a more difficult boss fight is in order as well as Izzy glows and the other ones suggested by other people, basically buff up all the bosses difficulty like in X3, on Xtreme, regardless of how many hours left, while making the hours slightly increase their difficulty only spiking toward critically insane on the last handful of hours and increase their health. Bring the difficulties to the boss rush, and slightly increase the other Sigma bosses for consistency. Again, for those complaining about the difficulty, this is on Xtreme, where I didn't really feel a difference. Keep Black Devil's one-hit kill on Xtreme. This will provide a sense of epicness like the nes-era where you completed insane difficulties feeling like Jesus.
Then theres text scroll, and cutscenes. For those who have already beaten the game once and seen the cut scenes, they would like to press start to skip them, (not the Alia dialogue, that ik you've fixed) like in X6. The text scroll is also somewhat annoying and if could be made like X6 soundwise. I don't think it's necessary to add the unused sound effects after the X4 crisis of "Its time to get serious!" somewhat annoying sound effects, I think X5 has it pretty much perfect, except for the squishy wall jump sounds
,could you instead replace the sound; with the wall jump sound from the SNES ,to keep up that epic experience.
In terms of weapons, make Skivers weapon attack wider upwards and make it so you can actually influence the direction it travels diagonally. Make the Spike ball fire and recoil faster, but this might make Sigma's final form easier so slightly decrease the damage to the bosses it affects. Make the Giga Attack trigger the purple blocks upon execution due to how easy it is to kill Sigma with the attack. Make Zero's shredder attack actually hit the target.
Probably the greatest thing you could also do is bring back the SNES era life bars (and an option to enable/disable them), in this beautiful hybrid created here and add the colors/fading colors to it: http://drake117.deviantart.com/art/X4-Life-bar-interface-175213264OH man I would really love you then.
Oh and one more grand thing! When you beat the game 100% on Xtreme with the best ending, when you start up the game and are at the game start, continue screen, option menu, the game replaces the background with the highest quality image of this!http://vignette2.wikia.nocookie.net/megaman/images/a/aa/Normal_mmx5promo.jpg/revision/latest?cb=20100420002539
This will be like Super Mario World when you collect all the Yoshi coins, adds an unlock-able, and will greatly increase the games replay value, as theirs nothing to unlock after completing Xtreme mode. Also I've noticed that upon selecting Xtreme and rebooting it turns back to normal which I find as an error.
Also if you could add X7's Sigma theme to play randomly on Xtreme or an option to enable/disable that:https://www.youtube.com/watch?v=70pQuYMgEFI
In addition on Xtreme add the unused soundtracks found here!https://www.youtube.com/watch?v=x4hQK6KoXRI
And if possible an option to add an enabling of the soundtrack remixes of X5 from this album into the game on Xtremehttp://maverick.ocremix.org/
These modifications will make the game perfect, and I honestly can't thank you enough.