Good show but writing doesn't make sense

1. Tomorrow people are humans

Despite how the show writers spin this, these tomorrow people are humans. Yes, they do have supernatural powers but we have humans who have other less powerful unique traits too. People with photographic memory that allow them to recite pi to the 1 millionth digit are still humans in my book.

2. The notion of one species of human replacing another is wrong

Despite popular conception, many studies suggested that Neanderthal did not simply get replaced by homo sapiens but rather intermixed and merged.

The same thing would've been expected if these tomorrow people mix with normal humans. There would've been no extinction of humans but rather more and more people empowered with these supernatural traits.

3. Why are breakouts only happening now?

This show did not explain why people suddenly get supernatural powers. It's not like it just came out of our genetics all of a sudden because most of the tomorrow people do not share a recent common ancestor. It's too unlikely for such a show of convergent evolution within such a short time frame.

4. Plot writing is too weak to handle supernatural powers?

Often times in the show, I am led to believe that the writers did not think through how teleportation affects their plot. Taae that scene with Ty Olson taking a bullet for Charolette and Cara for example. It does not make sense in a few ways:
1. Cara did not port out
2. Ty Olson did not port behind Jed and wrack him with a club
3. Jed did not bring with him a mobile D-chip to protect himself
4. Jed did not bring in a whole army of supernaturals to wipe the floor

There are other things to left to consider too. For instance, nothing in theory should stop the Founder or other supernaturals to just jump into their enemies' house and end them.

Granted that Russell did just that and kidnapped Jedikiah alone, I was left to wonder why his people didn't do just that in long ago and in force?

On a similar rein, why was Jedkiah allowed back in his house to hack into the Founder's mainframe when the Founder could easily port into his house and mole/wreck it long before that scene?

And ultimately, given the insanely ruthless nature of the Founder, why did he not scour everyone's minds for secrets? He did not need people's willing participation after all. There are way too many sabotage happening in ultra for that measure not to be taken.

5. That doomsday machine

It's a huge deus-ex machina. Stopping time so that the Founder can kill all humans by bypassing his no-kill genetic protocols? That's a feat of over-engineering in plot construction.

It'd be much easier for him to disable that no-kill switch just like he did with John or use indirect methods.

Also, if being able to kill is what that machine allows, then it wouldn't be about killing humans but about killing anything - including tomorrow people. The show writers missed that big hole.

6. What do characters want?

Hillary and Jedikiah are evil then not evil then evil then not evil then evil.

Russell was cool and loves some supernatural chick. Then he betrays everyone and gets happy with some whining girl who complains about everything.

7. What are characters thinking?

Characters in the show often do not comprehend their situations very well. The Roger messiah guy came back and want a family dinner and everyone's up in arms? Come on, give him a few days to catch up with the world for Christ sake!

Natalie is also the result of bad plot writing. It's okay to have a trouble-maker but she's allowed to cause too much damage unchecked. First, she got her gang juiced up on some kill switch, then she came back blaming people about her problems, and then she betrayed everyone. Guys, when you got rebellious elements in a group that has a stake in delivering your leader to the enemy on a silver platter, you do not let them talk smack over and over again and sit on your soft belly while you are busy with something else.

The scene with the mom coming in to save the dad was cool but once she gained the advantage, she decided to waste time checking out an obviously alive dad instead of neutralizing her threat completely. Cliche setup of a hostage situation that many movies fall victim to (even Cloud Atlas had this problem in the scene with the black slave fighting with Tom Hank's character).

8. Why aren't characters migrating?

The tomorrow people movement is built around the desire to be living on the surface. The world is a very big place and of all places, they chose to be living underground in the same city as the HQ of the company that wants to experiment on them.

Guys, why not try living somewhere else?

9. Jedikiah did gene therapy on himself

It's hard to imagine Jedikiah did not find the genes themselves when he already developed a serum to neutralize the powers. One would imagine the serum would've come after the identification of the genes.

Furthermore, the genetic markers used by the Founder many not highlight the entire array of genes responsible for the powers. It may only target a few. Even if we assume gene therapy is a perfect + rapid process and that there aren't any developmental biology (i.e. even with the DNA, you may still need development of the organs in the fetal stages), it's still a bit forced as a plot point.

I think 4400's deux ex machina on a unique neurotransmitter is more plausible...