Mega Man 9 easily has the best weapons of the series, mostly because they were far superior than the Mega Buster in practically every situation i.e. they were overpowered. The stage design aside from Wily Stage 1 never forced you to use any, which even then I don't see why this would qualify as a bad thing. That said, Mega Man 9 actually did have brilliant stage design and enemy placement which encouraged you to use your special weapons over your buster, and if you didn't notice this, I'd encourage you to replay Mega Man 9. Mr. Perfect and good Time Attack scores emphasize this point well.
The weapons are "The Best" huh?
Laser Trident= Basically a stronger megabuster, okay this one is good.
Black Hole Bomb= Slow moving projectile that sucks things in, it can be useful but its more conditional.
Magma Cannon=Atomic Fire that shoots in three directions, wow totally original 10/10 capcom, I never found any use for it.
Concrete Shot= Conditional, forced usage for stupid lava lasers in Wily 1 and stupid lasers in Wily 4, runs out of ammo too quickly to be of much use.
Hornet Chaser= Good for getting items and killing Mr. Angry Rock but not much else.
Tornado Blow= Forced Usage in Wily 1, can damage fire dragon miniboss but its not that great.
Diamond Barrier/Shield/whatever= Its a stupid shield. Good for telly grinding but [tornado fang] barriers.
Plug Ball = Okay it hits enemies on the ground guess what its not good for much else.
The stage design should not under any circumstance force you to use special weapons, you should always be able to rely on your buster since that is the most handy weapon in the game. That's not fair to people who either use said weapons to kill enemies then you're [tornado fang]'d because you don't have enough to move on. It wasn't a good idea in Megaman 1 with the Magnet Beam (Though the Weapon energy respawned IIRC, so it wasn't too big of a loss but if you didn't pick it up before hand you would be screwed.), it wasn't a good idea in Megaman 2 with the Boobeam traps (Not level design but its still a [parasitic bomb] boss.)
You say just Wily Stage 1, but Wily Stage 2 had those bullshit jumps underwater where you either needed to be pixel-[tornado fang]ing-perfect, use concrete shot or Rush Jet (If you could get rush to you without him teleporting away because of how [tornado fang]ing narrow those spaces were), or taste death by spikes.
And again, Wily 4 and the lasers you have to block with concrete shot. Unless you just suggest I run through them and take damage.
I'll say it again, Megaman 9 is terrible, the level design is weak, the game is basically photographic proof of capcom giving head to megaman 2 because its hailed as the best for some unexplainable [tornado fang]ing reason. Its totally cool that some people enjoy it but I don't get how people would want more games like it because it honestly isn't very fun.