You have missed out big time.

Even the incredible Mega Man 2 can't compete with Super Mario Bros 3. We got Mario 3 almost a year later than MM2 here in the States, so it's weird to think of them being the same year.  It was actually Mario and Mega Man 3 later in 1990 that pulled me away from my new Sega Genesis for awhile.

And in the arcades, Ghouls n' Ghosts for me.

It's Mario Bros 3.
The sheer quantity and quality of content it offered was off the charts. It was like if a game came out today with a 100 hour long campaign of GOAT gameplay.
To this day, 35 years later, it remains one of the finest 2D platformers ever made.

Biggest Cultural Impact: Super Mario Bros. 3 was clearly the most impactful game originally released in 1988 for reasons we all know by now and don't require further explaining on my part.

The Game I'm Voting For Anyway: Too bad though because the oft-missed little gem that is The Guardian Legend combines aerial combat of the highest quality with the exploration emphasis of adventure games, voice acting (yep, on the NES!), and a female protagonist to emerge as my absolute favorite NES game by a wide margin. I vote for it out of defiance. Nearly invisible and long-forgotten though it may be, it deserves to be the winner! This game earned better than its commercial fate!!

Feast your eyes (and ears). Here is The Guardian Legend, the greatest NES game ever made. The next game I want to see re-released in streaming form for the NES Online on the Switch rather than more of the garbage we've been getting lately:

Did you just give Mario the middle finger?

I play Super Mario Bros 3 at least one time each month. It is the first game I remember playing (probably played something else before that did not stuck) and very few games can match it today. For me it is the best game of its generation and a top 10 games ever. Game of the year absolutely.

Obvious Compile is obvious! The shmup sections screamed "Zanac/Aleste" audio-visually.. and that's not a bad thing! 2 minutes into the video and I thought "This feels too Zanac-like to not be a Compile game, let me rewind and see the developer. Yep!"

I'm impressed by how it mixes two genres (Proto-NieR?) while looking as good as it does on a low-end hardware. Plenty of great overlooked/forgotten games from that generation...

I did mention Aleste which is the closest game in this thread to your pick! Zanac MSX is one of my first ever video games, the crazy thing is that Zanac Neo on PS1 which was supposed to make you feel nostalgic, is now itself a nostalgic game. Time is brutal.

Super Mario Bros. 3 and Mega Man 2 are still on my Top 50 list so I'd say these games definitely stood the test of time.

Never was a big fan of Super Mario Brothers 3. So go with others and say Dragon Quest 3 even though I never played all the way through but I am looking forward to the remake. Also, Final Fantasy 2 really isn't that bad beat it twice and enjoyed it.

Does best Italian accent. Oh nooooooo!