I personally think the charge shot is balanced in MM4, it's in MM5 that they went way overboard with it, and as result the charge shots of all games are put in the same bag even though they're different. There are many factors in play: charge time, size of the charge shot hit detection, speed at which it travels, whether or not you're allowed to shoot more projectiles when a half-charge in on the screen and how many, but also invicibility frame time of bosses (and more).
MM5 changed most of these factors favouring the charge above else; and it's worth noting that MM6 backed down (though probably not enough) on several of those factors including the most important ones: hit detection size and charge time, making MM6's charge an "in between" of 4 and 5.
My Protoman hack of 5 modified several of those factors and hopefully make MM5 a little more balanced in that regard, for one thing the reduced charge shot size means that you actually have to aim with it, which is also the case in 4.
Anyway, there are plenty of situations in MM4 where if you insist on using the charge shot only you're going to have a harder time, the most obvious example being Dive Man: if you don't use the regular shots to destroy his missiles as they spawn, you're going to get overwhelmed pretty quickly, meaning you're pretty much only allowed to charge and unleash a charge if you time it well after dodging Dive Man's dash. This entire dynamic is lost if you get rid of the charge shot entirely. Kabatoncue and Moby are also good examples, Kabatoncue's pillar respawning faster than you can destroy it with charge shots (so it's a bit ironical to get rid of its 2nd encounter where it was a pro-regular shot enemy), but if you bring the pillar all the way down you should have time to hit him with a charge. Moby also goes downn much faster if you stick to regular shots, but when you're dodging his missiles, this is when charging becomes worth it.
Skull Joe's collapse feels to me like it is the whole idea behind his design, one possible change would have been to have regular shots harm him, but give him 3 HPs and he'd die after 2 collapses with regular shots, but instantly with the charge. Also to me the whole point behind Pharaoh Man's fight is that he is a mirror of MM: "oh you can charge? well I can charge too, let's see whose is better", and when he doesn't charge and jumps around with regular shots, that is also when the player is encouraged to user regular shots because Pharaoh's more likely to dodge the player's charges then.
I'm not saying it's perfect but my point is the charge shot in 4 isn't nearly as bad as some other games like 5, and imo too many dynamics are lost if you get rid of it entirely. I would have rather seen subtle changes that encourage smart play and switching between regular and charge shots more often, rather than getting rid of it entirely; turning the game more into what MM10's charge shot is with Protoman for instance, in which inv frame time of bosses alone encourages regular shots, unless the boss behave in such a way that he's not often likely to dodge the charges. Of course I understand that reducing inv frame time of bosses too much is also an issue because it means you can spam their weaknesses even quicker, that was an issue to me with hacking MM5 for instance.
Edit : btw - it would be a good idea to make a Rockman 4 version of the hack, that is if it would be compatible with Puresabe's lag reduction hack of the game (which only works with RM4)