G3/-X is a 100% technological manmade creation with nothing taken from the unknown, the Agito or otherwise; the biggest influence just being “it looks like Kuuga”. Tragically, this is why it sucks!

Same deal with Ixa, now with 100% more Catholicism

I did at least like the transformation of G3 how he literally puts on the suit, not sure if Metal Heroes did it first though!

Depends on how you define the "direct connection", but here are the ones I know:

X: The technology that created him came entirely from his father; the bad guys were after it though.

Amazon: His power-source was given to him so he could protect it from the evil organization

Super-1: As has been mentioned already, his powers were made for space exploration.

J: Is given power by the Earth Spirits to fight against the alien invaders.

Agito, you mentioned that one yourself.

Blade: Maybe? Maybe not? The cards are technically the bad guys?

Hibiki: He's just a demon; he didn’t really gain his power from anyone.

Den-O: Uses a system that incorporates Imagin but wasn't developed by them so I think he counts.

And with Phase II... wow, there's not a lot here, huh? Maybe Ex-Aid? Zi-O, kind of? I haven’t watched Fourze so I can’t say if his switches are connected to the baddies somehow. Wizard uses magic stones sometimes given by the evil guy but magic isn’t inherently evil so him too?

Zero-One counts though, the Progrise Keys were made to counter the Ark.

No no, a lot of those examples very much count.

As the overlords were once the same entity and are just two sides of the same coin, the Lords and the Agito very much have the same basis.

The Rouse Cards being the monsters is as literal as you can get, but even beyond that the belts are directly based on Joker’s belt.

We don’t know much about Den-O’s belt but, yeah, it is quite literally kaijin in a rider suit vs kaijin.

Heisei 2 is littered with examples. Dopants, Greeed, Zodiarts, Roidmudes and Ganma all use or are made of the Riders’ gimmick items; the Wizard riders all have phantoms inside of them; Lockseeds originate from Hellheim; everything in Build is rooted in nebula gas and Evol’s machinations. Ex-Aid is a bit iffier but Emu is able to henshin at all due to having game virus, and the momsters all originate from Gashats. This is also the season where evil Riders really started to take over as the main villains, so make of that what you will. As for Zi-O, the Another Riders are made from corrupted Ridewatches and arguably the main villain is Sougo’s future self.

The Progrise Keys may have been made to counter the Ark but Ark and Zea are two sides of the same coin and keys get used by both MBJR and Thouser.

Den-O is a technicality. Den-O's powers come from Ryoutaro being a singularity point, but in the series proper, everyone who transforms uses an Imagin as an aide.
So it's skirting a line since he doesn't need the Imagin, but he never gets results without them.

Also, I was wondering. Switches. Fourze uses them, the Zodiarts use them. But are they really similar in powers or just similar in gimmick? It's not as closely knit as Gaia Memories and Medals were in the proceeding series. Are the Switches in Fourze really tied to the villains?
(Note: I haven't watched Fourze since it's aired, so it's been a while)

More like the astro switches and zodiarts switches were based off of the core switch and its original intent was to use it as a means to reach the Presenters if I recall, only to be repurposed when the Zodiarts threat became a thing.

Yes, both Switches come from the same source.

I was wondering, when you picture Hikawa/the secondary Rider from Agito, do you see him as G3, or G3-X?

Personally, when I think Agito, I think G3-X since that design had a stronger lasting impression on me, but G3 was around for quite some time (Even debuting before Agito himself), so I was wondering.

Honestly, I picture him out of the suit. That's the iconic version of Hikawa for me.

Fair enough. I love the guy