As for the 06 romance, I think it's kind of a Roger Rabbit mentality. The people in charge don't really see a rabbit and a woman together...they see two cartoon characters together.
I believe it has been mentioned that Sonic's pre Sonic 1 human girlfriend was partially inspired by that Roger Rabbit mentality. As far as Elise, an anime design might have worked since Sonic didn't look out of place in Sonic X. But they went for a realistic design and in a game that also had Amy in it that was 15 years into an existing franchise.
Returning to the Amy discussion, there's a lot of things that were there the whole time with her but don't get focused on. One is her comment at the end of her story in Sonic Adventure: "Just watch me. I'll make that Sonic respect me!" It's interesting to think about the actual trajectory.
-Sonic Adventure 2. Amy rescues Sonic. While it's not a thing Sonic would hold over her, she repaid the debt of having to be rescued. Her "will you marry me" is met with a No.
-Sonic Heroes. Since a rescue didn't work, Amy challenges Sonic to an anime rival battle. The answer is still No to marriage.
-Sonic Battle. She mistakenly assumes that taking care of Emerl is Sonic presenting a secret test of character to see if she'll be a good mother. In her zeal, she takes up boxercise. While a lot of the focus the game gives is due to her obsession with using boxercise to lose weight, she takes it up in the first place to protect Emerl. Sonic & Tails explicitly comment that she's getting stronger. I think it's worth noting that the people who are known to have martial arts training are Knuckles (one of the strongest characters in the setting) and Espio (a literal ninja).
-Sometime after (unsure on the first game where it happened) Amy started asking Sonic out instead of immediately jumping to marriage. It marks a shift, especially since while Sonic will immediately say no to marriage (makes sense considering they aren't adults) he'll often get flustered instead of turning her down when dating gets mentioned.
-Sonic '06. Elise gets kidnapped a billion time but one of the times she gets kidnapped it's Amy who does the rescue. The two of them have a talk and discuss love, not knowing they're both talking about Sonic. Later in the game, Amy doesn't flip out when Elise gives Sonic the kiss of life. She's able to be mature if someone else catches Sonic's eye. Then 06 decides to 06 and erase itself from the timeline.
-Sonic Unleashed. Over the course of the game, there comes a point where Amy asks Sonic if he'll go out with her after he saves the world. The answer has no affect on the game...
-Sonic and the Black Knight. Sonic starts the game with two chili dogs, which doesn't sound like that big of deal. At the end, Amy's chiding him because she thinks he's making excuses instead of truthfully recounting he got sucked into a storybook. Excuses for missing their date. She had finally gotten him to agree to a date...and she feels like he stood her up.