So many plot holes!
I love the show. I adore the show. But even I am aware of the fact that there are SO many plot holes.
1) The New York hybrids had all of their memories of their past lives while the Roswell hybrids had no memories except for little flashbacks here and there and vague abstract recollections. It was established that the NY hybrids were the "rejects" and that the Roswell ones were not the rejects. Therefore, wouldn't it make more sense for them to make the Roswell ones retain all of their memories (via memory programming and stuff) and make the NY ones forget all of their memories? You know, so that the Roswell ones will remember who they are, use the Granolith, etc. without the rejects almost messing everything up for them, like they almost did.
2) Max had an immediate and strong attraction to Tess, to the point where he wanted to rip her clothes off the moment he saw her. Wouldn't this same carnal desire be present with Michael and Isabel long before Tess and Max met? It seems that Max and Tess being physically near was euphoric and intense, to the point where they were magnetically drawn to each other just by being in the same room. Why did Isabel and Michael start to experience those sexy dreams only when Tess came into the picture? And also, how is it that at the beginning, Max could barely keep his hands off of Tess and then suddenly, he was all indifferent to her? I get that he loved Liz, but, that didn't stop him from kissing Tess because he couldn't help himself. Then, suddenly, the spell just wore off and he was all like "Meh."
3) Liz didn't sleep with Kyle and when Max found out that she didn't actually sleep with Kyle, it was just never spoken about again and no mention of the time travelling Max ever came up after that point. I mean, he came with a serious prophetic message... did they just never bring that up ever again?
4) When Max tried to rejuvenate that old man, Max died, and then the old man inherited Max's body and mind. But it wasn't the real Max, was it? The real Max was dead. Perhaps just a copy of Max's memories transferred over to the old man? Similar to meta crisis doctor in Doctor Who. Was it Max... or was it a copy of Max with Max's memories? Hmm.
5) They talk about how beautiful Vilandra was and hint that the aliens may have looked different, but, were still beautiful. Ie, Max saying that Tess was the most beautiful girl he'd ever seen back on his planet. Yet... every time we see an alien from the planet Antar, they are a stereotypical grey alien. When the hybrids are in their pods, in the flashback scene Michael was listening to, we saw grey aliens protecting the pods. When Max asked that shape-shifter to fly the UFO, he shifted back to his real form, and we saw that his real form was a grey alien, basically. They also showed Nasedo's true form which also looked like a grey alien form. If that's so... then... grey aliens all look the same, so, how is it that Vilandra and Tess's (Ava's) beauty was something noteworthy if everyone just looked like a standard grey alien?
6) In the holographic message that Max and Isabel's mother left for them, she clearly knew how to speak English. Then, wouldn't it make sense that the encrypted alien book also be translated into English? I mean, they cloned the royal four, made two copies, sent the rejects to NYC and the Roswell ones to Roswell, and... the NYC hybrids had all of their memories despite being rejects, and, the Roswell ones were clueless, unaware of everything, and had an encrypted book that could only be decoded by a mega super-computer. Just seems like it would have made more sense to, I dunno, program the Roswell aliens with knowledge of their native language and memories, you know?
7) Are they reincarnated? Are they merely hybrids that have the royal four's DNA? Are their memories / knowledge of themselves programmed or is it on a spiritual level because they reincarnated and have the soul of the royal four, or just the DNA? Similar question to the Max question I have. When Max was trying to heal the old man, did Max die and was that just a copy of Max's memories, or was that... Max? So many questions, no answers.
The way Tess kept talking about how it was their "destiny" to be together because they were together in a past life makes me think it was more on a spiritual level and reincarnation was at play.
8) If Tess hatched in the same place as the other three, in Roswell, and if Nasedo cared for her all that time, why didn't he just reunite her with the other three when they were younger so that they'd all grow up together? It's not like Roswell is such a huge town and the other three would be hard to find... I mean, as I understand it, Tess just took a bit too long to hatch. The other three would have probably bonded with her as children because they all have that sacred alien bond, so...
I'm sure there are many more plot holes, but, it's becoming tedious to try to wrap my mind around some of these, so, here are just a few.