NSFW/NSFL WARNING: Spoilers and potentially nauseating content (demons, occult, conspiracy)
Before you explore my theory, you should be familiarized with (or at least open to the notions of) concepts regarding mind control and satanic ritual abuse, specifically Monarch Programming. These fringe concepts are based upon ideas regarding conditioning in psychology. There may be other unfamiliar topics, but these are the most important. Research these topics at your own risk, they have potential to harm you psychologically.
FF8 is one of the darker installments in the series. It has spawned a number of fan theories regarding the message. I believe one possible interpretation is that Squall and his allies were carefully manipulated from early childhood to be characters involved in future conflicts.
FF8 touches on a number of esoteric ideas. Edea becomes full-on possessed by Ultimecia, who has characteristics of a diety (doesn't something similiar happen to Seifer and Rinoa during disc1 as well?). Ellone is a type of clairvoyant. In disc 4, there is time travel and parallel dimensions. Body doubles are used during the mission at Timber. There is also a slight emphasis on the technology, study, and combination of the supernatural elements.
The team spends the early developmental years of their lives under the close supervision of Matron. This is crucial, because this is the time when their young and impressionable minds best receive conditioned triggers. The trauma endured by the children is symbolized by Matron's ominous attire and Squall's incessant crying in the rain. These crying scenes are more important than initially received; remember, a squall is a "short rainstorm", and this is a recurring storm scene in a normally fair-weathered world. This is perfectly congruent with the frequent and repetitive trauma desired to create mind-controlled individuals.
After the orphanage, they all go to Garden, which are nothing short of indoctrination centers in the main story. This is where the ego develops; the conditioning of the early life becomes subconscious. The story makes no effort to explain why the orphans conveniently went the same route. Matron and Cid are married, so it is as if one person always controlled them. This conflict of interests isn't explored rationally at all in the story, there is only a bit of emotional sentiment attached to the fact that Matron is the enemy. It would be safe to assume that the orphans were destined for Garden all along. Also, the idea that junctions somehow cause memory loss could be misinformation, or a symbol of the transformation that occurs to the psyche of a mind control victim.
There are a few more symbols that lend creedence to this theory. The opening cinematic can be interpreted as an unconscious recollection of the past. The field of flowers is an unrecognizable conditioned image, and the phrases that pop up are suppressed thoughts. The unconscious events culminate into Squall receiving a scar. Secondly, the assasination attempt of Edea is an allusion to the JFK assasination, which is an esoteric complexity in itself. SeeD is a possible reference to Starseed ideologies.
TL;DR: Squall and companions were victims of satanic ritual abuse in their early years, allowing them to become excellent members of SeeD.