What is the next step in engine/chassis development?

I see smaller CC engines for both classes, just like the 500cc, the 450 will become a relec.

I could write a novel on this stuff, but in the interest of time, here are some high level points to answer your questions:

Is triple clamps flex a major part of a bikes handling? 

It can be significant. We make clamps as stiff as possible in all directions except front to back. That makes them handle precisely and keeps the fork tubes better aligned for less binding, which ironically makes it more comfortable despite the clamps being stiffer. The stiffness front to back is tuned for comfort and can make a big difference in feel on the track.  

Some people have been complaining about a bikes suspension and handling being bad. Can adding more triple clamp flex give them what magic cure they are looking for? 

There's no magic cure for anything; it won't fix all your problems, but the right flex can certainly make things a lot better for comfort and handling. Clamps are perhaps the largest change you can make in terms of stiffness changes on the bike. That change will vary significantly by who made the clamps you're using, though, and won't necessarily be a good thing... 

Another part is Fork tube flex could be a major part of this too.

Everything flexes to some extent. Fork tubes are a big part of that, but there aren't many options for swapping those out for tuning. Here's an old blog post about that: https://www.luxonmx.com/blog-luxon-fork-tube-stiffness-flex.html 

Frames also use the motors for part of the frames bracing and strength and I see some are completely removing motor mounts so the frame actually flexes more. Is this transferring a load in one area of the frame that is now a place that will eventually fail and crack?

Possibly. That depends on a lot of factors, and will vary bike by bike, so I can't give a blanket answer for all situations. I wouldn't recommend removing any engine mounts entirely, and it likely wouldn't be a good result for handling anyways. Aftermarket mounts with a hole in them have more of a mental effect than a physical one. They flex more, but not much more at all. Doubling the flex of something that hardly flexed to begin with doesn't do much! We have rubber isolated engine mounts coming out that are a different story. There's enough give to actually feel a difference and remove some vibration, but it still provides the structural support the frame needs and maintains precision in handling. 

I believe Yamaha has been developing an active rear suspension system, it actually changes damping when the rear brakes are applied. This allows the rear of the bike to settle instead of hopping in braking bumps. Really quite ingenius!

That doesn't sell new bikes though. All these OEMs are pretty much always going to be NEWER, FASTER, BETTER! 

Yamaha has already done that for a short period on production bikes with a cable going to the shock from the rear brake pedal along with Z spokes 

Yes - BASS - that was my obscure sarcastic joke, sorry!