I see so many people pointing out Power Stone as a poor weapon, but it's actually one of the more effective and more fun weapons to use in MM5. The game was designed around a lot of enemies that only take one hit to kill, and often putting them in areas of the room that are out of reach initially, so that you have to wait for them to close in on you before you can attack. Power Stone can clear a lot of these rooms in one use, and even aside from that there are a lot of really great room layouts that take its shot pattern into effect. I played a run of MM5 a while back where I tried to use the RM weapons more effectively, and Power Stone was a surprising hit. I recommend you try to experiment with it more, you may find it worth your while in the end.
As for the points, I'd have to say that saying "it didn't have [blank]" is not a very strong argument when the alternative isn't any better. For example:
1) Sure, there's one fortress, but it's the worst fortress of the entire series. The stages are super short, it recycles two bosses from other Mega Man games (when there were only two others to draw from, yikes), and there's little to most of the stages (Wily 2 has three bee enemies in it and a forced Rush Jet segment that...requires no skill whatsoever).
2) Bad to pick out MM4 as your example, as it had the most well-balanced weapon set of the series until 9 came out. Pharaoh Shot is aimable and chargeable, Ring is piercing, Dust can multi-hit, Dive can home, Toad is screen-clearing and ignores defense, Bright stops time, Skull is a barrier, and Drill is powerful, fast and can be manually ignited to get around certain defense layouts. Every weapon is useful and every weapon is UNIQUE, among the others in that game anyway.
Look at MM3's weapon set:
Search Snake - ground-traveling attack, can climb walls
Shadow Blade - projectile, fired in a straight line, can be aimed in multiple directions
Needle Cannon - projectile, fired in a straight line, fast attack
Gemini Laser - projectile, fired in a straight line, bounces off of surfaces
Magnet Missile - projectile, fired in a straight line, trajectory can be changed once without player input
Hard Knuckle - projectile, fired in a straight line, trajectory can be slightly altered by player input
Spark Shot - projectile, fired in a straight line, can freeze enemies, does no damage
Top Spin - aerial melee attack, incredibly glitchy with response to energy usage, trajectory of jump can be affected by enemies, hitbox inconsistent
Suffice to say, a lot of it is "samey", and there are a couple that are complete duds. Top Spin could be viable if there was any situation in which a projectile would be worse than a melee attack, but that's never the case, and it's so glitchy that it's a danger to ever use it in the first place. Hard Knuckle is too slow to be effective in most encounters. Spark Shot doesn't actually damage anything. Gemini Laser is both slow and weak, and if you miss your shot you have to wait for it to run out before you can shoot again or switch weapons. Needle Cannon is just a fast Mega Buster, and the game isn't designed with the Search Snake in mind, as there are very few situations in which you're above enemies and that's where the snake movement pattern would be most effective--as it is, it's again too weak of a weapon. Magnet Missile and Shadow Blade are the only two that I could ever see being useful throughout the entire game.
I'd argue that MM3's weapon set is by far the worst of the series. You have 7 projectiles that all fire directly in front of you whose specific characteristics are mostly not very effective, and one melee attack that's glitchy and dangerous to use.
3) No Wily Capsule, but the final boss of MM3 is beyond pathetic. You can stand underneath him indefinitely and not get hurt, and then he dies in one hit. I'd take any of the series' Wily Capsules over this fight (except MM7, cause that fight's so annoying).
4) Rush Jet was completely broken and made every platforming segment in the entire game skippable. Changing it to the MM4's Jet was definitely a much-needed change.