Super and Zero Mission can be beaten in 4 hours or less (I've beaten both in about 3) without cheats. Fusion takes about the same amount of time. And regarding difficulty; it's a Metroid game, they aren't very difficult.

If you want a difficult game, go play Mega Man Zero 2. Its good, but really hard (except for the easy final boss).

Honestly, I'd recommend all of the Mega Man Zero games to anyone. They're quite fun.

MMZ1 is harder than the second game though

Mostly because of s*** mission objectives

Tbh, I never found the first game to be all that difficult, I always found 2 and 3 to be more difficult.

3's pretty easy imo

Doesn't stop it from being the best though

I agree completely. Unfortunately, 4 wasn't as good, but its still a good game. Weakest one in the series IMO.

I don't even remember much from 4 other than the weather system (and I don't even know why that needed to be a thing)

Lunar Legend, hidden gem

I remember the Klonoa games being pretty fun...

for the love of god play mother 3
boktai 1&2 are nifty games that are hard to get a hold, but well worth it - the cart has a solar panel that has an effect in-game depending on if you're inside or out - there's some isometric mgs style stealth in 'em
gunstar super heroes is a good sequel to gunstar heroes - not as good as the original, but forimidable
final fantasy 6 advance is (probably) the best final fantasy, even if they butchered the music - there is a music remaster patch out there that can fix it if you want to play a rom / play on a flash cart
zelda ii does happen to have been re-released on gba - if you missed out on being a 3ds ambassador or don't want the virtual console version, the gba version is the way to go
sigma star saga is a damn fine scrolling shooter
the mega man battle network series is a series i have extremely fond memories of, even if most of all the games are complete bs - the combat system is really unique & great, and i still think about it on a regular basis
astro boy: omega factor is one of my favorite licensed games of all time - just a great treasure shooter
warioware: twisted! is the best warioware game i don't care what anybody else thinks

-not gba-
shantae and metal gear solid on gbc are both stellar
link's awakening dx is my favorite zelda by far

idk if this has already been mentioned but castlevania: aria of sorrow is a great game and you should definitely play it
my physical copy just arrived from eBay a couple of days ago

Just be warned that trying to get all the souls will make you cry