Perhaps it could be Spike in a very different and creative interpretation. Since Spike has a close bond with Twilight, some fanfictions might take a unique turn and make them have a more romantic relationship which results in a baby, although this would be a very unconventional take.
Another option could be a completely new character created just for the fanfiction. This new character could be a powerful unicorn or an alicorn from a far - off land who met Twilight during one of her adventures and they fell in love.
One possible plot could be Twilight adjusting to motherhood while still having her magical duties. She might struggle to balance taking care of the baby and her studies or helping her friends. For example, she could be in the middle of an important spell research when the baby starts crying, and she has to quickly shift her focus.
She could marry Flash Sentry. He has shown an interest in Twilight in some storylines, and their relationship could develop into a marriage. They could bond over their shared experiences in Canterlot.
Fanfiction often takes creative liberties. In the case of 'mlp twilight baby fanfiction', it may involve Twilight being reimagined as a baby. This could lead to all sorts of interesting plotlines. It might include things like how she discovers the world around her for the first time. It could also involve her being in situations that are both humorous and heart - warming, such as trying to communicate with her friends in a baby - like way or getting into innocent little misadventures.
A dark magic - using villain from the MLP universe could also be the one to betray Twilight at the wedding. This villain might have infiltrated the wedding planning under a false guise. They could then use their magic to turn Twilight's friends against her during the wedding, making it seem like Twilight has done something wrong when in fact she is the victim of betrayal.
It could be Discord. He loves chaos and might think it's fun to kidnap Twilight and see how her friends react. He could also be after her knowledge of magic to cause more mischief in Equestria.
It could be Hinata. Since they are in a relationship in the original series, it would be a natural choice. Hinata would be a loving and caring mother, and her gentle nature would be a great influence on the baby.
It could be a dark magic user who doesn't want the human - turned - Twilight to succeed. Maybe this antagonist sees the new Twilight as a threat to their own power or plans in the pony world.
Another option could be an alien from Starfire's home planet. This would add an interesting dynamic as the baby would have a strong connection to Starfire's alien heritage. It could also bring in some unique storylines about the alien culture and how it affects the baby's upbringing. Maybe the alien father has certain powers or responsibilities that are passed down to the baby.
Maybe it's a mysterious character. The fanfiction could introduce a new character as the father, someone with a hidden past or special abilities that add an element of intrigue to the story.
Another option is that the father is a character from a different species or planet that Ahsoka met during her travels. Their encounter was brief but passionate, resulting in the baby.