Here are my favorite pairings and my thoughts on them:
Littlefoot x Cera: This is my favorite shipping because I love the complex and dynamic relationship between them. First of all, I love that Littlefoot helped bring out the good side of Cera despite her father's racist influence, and most importantly taught her friendship and kindness that she hadn't really experienced before. Conversely, I think Cera does a great job in getting Littlefoot to think about things with her never-ending ability to question his beliefs and get him to really think about them, often making his beliefs even stronger in the process.
Plus, I like the fact that they naturally complement each other. I think Littlefoot's patient and understanding nature would be a great compliment with Cera's stubborn and prideful one, plus that the two of them have shown really strong loyalty to each other despite their numerous disagreements. I think it would be really interesting to explore their relationship through a mated perspective, and I think their relationship would be very deep and fulfilling for both of them.
The future characterization and development is another reason why I really like this pairing. Littlefoot seems like he'd naturally break down the species divide in terms of marriage, just as he had in friendship. It's in his nature to consider the possibility that no one else has even thought of, and I think this shipping would really display his openness and idealism very well.
Conversely, I think this shipping would be a great step forward in Cera's character development. If Cera was in love with Littlefoot, she'd have a lot of tumultuous inner conflict. She'd have to grapple her emotions with her pride, skeptical attitude, and stubbornness, not to mention that her father was once an avowed specieist and would likely try to fight their marriage. If she ends up being with Littlefoot, I think this would give Cera an opportunity to really advance in her character development journey. Overall, I imagine a Littlefoot x Cera relationship to be filled with twists and turns and inevitable conflict, but their pure hearts and deep loyalty to each other would keep them true lovers till the end.
Ducky x Petrie: This is a pairing to me that just clicks naturally and just feels right. The two of them always seem really close to each other and have plenty of scenes featuring just the two of them. Also, they have a lot of traits in common that really make them mesh well in my opinion: distinctive speech patterns, small stature, naivete, caring, slightly fearful but usually cheerful, not domineering, etc. They seem to relate really well to each other in my opinion, and sometimes I get the feeling they have a mild crush on each other already.
In contrast to Littlefoot and Cera, I would imagine them to have a relationship with less character growth and development, but a more harmonious and amicable relationship with minimal conflict. I imagine that both of them would be really supportive with each other, especially in regards to Ducky's eternal optimism would likely help assuage Petrie's neuroticism. Plus, Petrie some of Petrie's bravest moments have been when Ducky is in trouble, which really show how much he cares for her. This is a pairing that I find really sweet, with lots of chemistry and emotional fulfillment, and I think will surely lead to a happy ending for both of them.
Chomper x Ruby: This is the hardest pair for me to explain why I like, but for some reason I find this one really appealing. I guess it's because Ruby and Chomper are often close together in the series and Ruby acts as Chomper's older-sister figure, and I like the idea of Ruby's older-sister feelings gradually turning into romantic ones as Chomper grows older (in my head-canon, he would unconditionally not hurt any of his friends as he grows up). They're just very cute together for me and I think would be a pair that gets along well.
Ali x Shorty: Here's a pairing that hasn't actually met, but I find them to be an intriguing pair nonetheless. They're both characters who've had to deal with pretty difficult circumstances, and they both seem somewhat jaded (though in very different ways) until they meet Littlefoot. In addition, they both tend to be insecure (again, shown in different ways), and often tried to hide their feelings before coming around with Littlefoot's help.
These two are characters that I couldn't really see getting together at the beginning of their movies, but after their learning curves, I think would work quite nicely. Shorty would become friendlier and Ali would learn to open up, and I could see them getting along well afterwards. They'd have a lot to relate to with their migrating journeys, difficult lives, personal insecurities, and learning important lessons through Littlefoot. Besides, this is a pair that I think is just cute together, and I'd really like to see them interact on any basis in any movie.
Part of the reason why I like all of these pairings as that each pairing is distinctly different from the other ones. Each pairing has certain qualities that I think would put them on very distinctive plot potentials from each other, and I personally think this arrangement of characters would lead to the most interesting romantic storyline without adding any new characters. I explore my take on these, primarily Littlefoot x Cera and Ducky x Petrie, as one of the prominent plots within my fan-fiction (shameless self promoting, haha

) and I might consider writing a Chomper x Ruby or particularly an Ali x Shorty relationship fanfic sometime.