There are a lot of games I tried out a lot later due to retro gaming. Some I had the benefit of playing on a PVM which helps the experience. (I will indicate which ones.) Here are some of the more well known ones:
Genesis
Phantasy Star IV - This game is often compared to Final Fantasy VI. I will say the music on PS 4 is incredible, at least as good as FF6, and I say that believing that Nobou Uematsu is the greatest composer in all of video games. However, as a whole, I think FF6 is a much better game. PS 4 is a good solid game overall, but it will never make it into my top 100, unlike FF6.
Shining Force II - I couldn't get into this game when I first tried it. I did play Shining Force I back in the day and loved it, but I first tried SF2 much much later. My main hurdle is I wasn't looking for a game with exploration elements in it. Once I got over that I gave it another chance, and now I love it even more than SF1. This is the second best turn-based tactical game ever made after FF Tactics.
Streets of Rage I, II, III - These are good, solid beat em ups. I still like Double Dragon better. Of the three SoR2 is the best and SoR1 is noticeably weaker than the other 2.
Golden Axe (PVM) - Loved the arcade version back in the day, but first played the Genesis version a few years ago. This is my favorite Genesis game. So much fun. I love coming back to this.
SNES
Super Punch Out - I first played this on the SNES classic. This game is fantastic and reminds me a lot of arcade Punch-Out which I really loved. It released a month before DKC, which is why I think a lot of people overlooked it and it also is a different style than the NES game.
Final Fantasy VI - I kind of tried this out when it was current, because I rented it. I got a little past the Opera House and figured I was close to done, based on how long previous FF games were. I finally went back to this many, many years later and got to finish this. There is a reason why some argue that this is the best FF of all time. I'm glad I finally got to complete it.
Earthbound - Another SNES classic, and I played this after beating Undertale multiple times, which may have affected the experience. This is a very good game, but I think Undertale is clearly better. That may not be a fair comparison since Undertale wouldn't exist without Earthbound.
Final Fantasy V - Similar to my Earthbound experience, I played FF5 after FF Tactics. Tactics is the better game, but the job system in Tactics comes from FF5. This is clearly a good game, that I would have liked more if I'd played it before FF Tactics.
Playstation
Suikoden 1, 2 (PVM) - I played these in order. Gotta say that Suikoden 1 was so much better than I expected. This game was a real treat and not like any other game I had previously played. I played Suikoden 2 for about 15ish hours and then quit. I played these games back to back and by that time I was Suikodened out. I'll probably have to come back to Suikoden 2 at some point and give it another chance.
Castlevania: SotN (PVM) - My favorite Castlevania is still Super Castlevania IV, but SotN is #2. I say this still holding that linear side-scrolling Castlevania is the style I prefer over Metroidvania. Still, SotN is just a damn good game. Glad I finally got to play it.
XBox 360
Lost Odyssey - Tried this for the first time just a few years ago. This felt like the Final Fantasy game that I had been missing since FF13 released. It was a lot of fun, but I kind of lost interest about halfway into the game and still haven't finished it. I need to go back and finish to see if the gameplay picks up again.
Gameboy Advance
(played these games on S-Video which also makes them look really good)
Astro Boy: The Omega Factor - This is the best action game I've played on the GBA. It's so much fun and a compelling reason why you want to play GBA games on the big screen.
Castlevania: Harmony of Dissonance - Another great GBA action game. It has a Metroidvania style, but the character uses a whip which I really appreciate.
Metroid Zero Mission - Great graphics, great controls, great music. Gameplay? Sucks! Overall an inferior experience to original Metroid in spite of the improved production values.