I'm confused at what the thread is about, relationships that were done well or just ships you support? I'm assuming its the former but some choices make it seem like its the latter.
First I'll go through his list and then post the ones I believe deserve attention that don't really get.
10. Felicia Hardy and Peter Parker (TAS)
While I didn't want them together in the end, this pairing was done so well through out all seasons of the show, at first you think the relationship is over but then it comes back again, They really did have great chemistry, would have loved to see another Spiderman season mostly because I was sure it'd have more romantic interaction between them.
9. Logan and Ororo Munroe (TAS)
Such an odd pairing but yeah I'd agree that it was done great, by the end of the episode I truly did feel bad for them.
8. Alicia Masters and Ben Grimm
Meh, it was there but it was done really poorly in the 90s animated show, it was done much better in the FF:WGHs though it still wasn't great. I like the pairing but it hasn't been done great in animation. WGH didn't do bad but could be better.
7. Nova and Silver Surfer
This one feels like a ship, SS was not interested in Nova at all, he was all about Shalla Bal in his show. In fact if you used the SS/Alicia Masters from the FF then maybe I'd agree, that was done pretty good there you could see maybe SS and Alicia could have something but his love for Shalla Bal truly felt tragic, he spent the entire season trying to get to her.
6. Bruce Banner and Betty Ross
Meh, I thought this wasn't handled too well.
5. Scott Summers and Jean Grey (TAS)
I prefer the TAS version over Evo, I don't know the Evo one felt kind of forced at times and Jean going out with the other guy at first didn't work out too well either.
There were times when I liked the Evo's version more but it was never followed through. It was when Rogue would show interest in Cyclops and Jean getting jealous, they showed it on various episodes but never culminated it with an episode, such a wasted opportunity. It would have been a great episode and maybe made me like this version better but it didn't happen so yeah TAS.
4. Mary Jane Watson and Peter Parker (MTV)
What? this one didn't make much sense at all. It was supposed to based off the movie continuity but it didn't fit with the characters in the movie. In the show MJ would always try to get all flirty with Peter and whatnot and Peter would just blow her off.
3. Lance Alvers and Kitty Pride (Evo)
I liked how they continued it through out the later seasons somewhat, I was sure it was going to be forgotten. It fits that universe fine. Nightcrawler was kind of forgotten and only brought back when they wanted, it started off ok but it was handled terribly later only using it randomly in the future and then forgetting it again. I mean it could have been an interesting love triangle instead of forgotten, and Nightcrawler ended up without no one pretty much because of it.
2. Wanda Maximoff and Wonder Man/Vision
Yeah, this one was actually pretty interesting, especially when both Wonder Man and Vision are alive at the same time, much more could have been explored too bad we didn't get to see it happen.
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1. Tony Stark and Julia Carpenter
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Another one that was just kind of there but was handled terribly.
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So yeah for my list besides the ones i really like from above I'll include:
Peter Parker Unlimited/Naoko/green goblin/shane/mj
This one was done in a subtle way but it was there. We know Peters love of his life is Mary Jane, but now that he is on counter earth he is living with Naoko and you can kind of see Naoko and Peter become close, shane really likes peter and not only does Peter have MJ on earth waiting for him but the green goblin is the husband of Naoko. It was clear the second season was going to go through with it to make the GG his enemy on counter earth.
MTV's Peter Parker and Indy
What I thought it'd be something annoying I ended up really liking it, she and peter made a great couple which only made her death much harder. Unlike MJ it really felt like both people were interested.
I know some people here mentioned Beast and that girl from TAS and yeah it was handled well but I also thought the one with the computer falls in love with Beast was a good romance episode.
Also out of all of Jonny's love interest in FF TAS the one that felt the best was Frankie/Nova.