They have two main issues really. Age (both mental and physical) and being siblings.
Their respective ages are a mess. Aqua/Gorou was around 30 y/o when he died and he has been in his current body for 18 years now, making his current "mental" age around 50, and his "physical" age 18. That said, he has already admitted that the line separating his current self as "Aqua" and his former self as "Gorou" was blurring, and his mind was being influenced by his current body. I honestly have no idea how to pinpoint his real age, and if this happened in real life, I would feel sorry for the poor fucker that got stuck in this situation. Now matter who you choose as a partner, the disparity between mental and physical ages are going to mess with it heavily.
Ruby, on the other hand, died at 12 y/o and is currently 18. Even if we account for arrested development from being hospitalized for most of her previous life, assuming her "mental" age to be ≥20 as a conservative estimate seems reasonable imo.
As I said, it's a mess. Needless to say, this is an important obstacle that they would have to figure out. Entirely on their own of course, since nobody except Deus Ex Ma- I mean, Crow Girl seems to know about their reincarnation.
That said, all of that pales in comparison to the elephant in the room. The fact that their current bodies are directly blood related. As twin siblings no less.
This, in my opinion, is the greatest obstacle between them being "together". Afaik, incest is
technically legal in Japan, with provisions made so that the younger party is not being abused by the power dynamics inherent in their relationship. But, not only does everyone and their mother know that they are brother and sister, there's a good reason that incest is ostracized in any modern society. Just procreation itself is risky, and the normalization of incest would be a devastating blow to the overall health of any people.
So really, they have 2 main paths. They get together or not. If they do, they have to choose whether lie their entire lives to keep it secret, or they go public with it, which would make them a target of criticism and discrimination the rest of their lives. Not to mention the possibility of having children...
In any case, unless the author wants to go down the... weird route, the fact that they share blood will keep them from being together; aka Aqua/Gorou will do his best to reason with Ruby that being a couple is just not feasible.
Part of me can relate to Aqua's feelings back at the start of the story.
No matter the way it goes, interesting drama will ensue. I'm looking forward to it.