Personally, my previous Evos had rim brakes and had very different wheels so even though my new one feels stiffer, it's hard to pinpoint exactly how much the thru-axle helps. The rear felt very different with the three different wheelsets I tried. I also have a 2014 Synapse Disc which has QR front and rear and I never had stiffness issues in the rear, but I have very stiff wheels on that bike with more spokes, thicker spokes, laced 3X. The front didn't 'feel' flexy because of the wheel but the QR was making the front rotor rub a lot more when out of the saddle. That was lessened with a DT RWS QR which is more or less the equivalent of a bolt-on skewer, but it's still not as stiff as a thru-axle.
One thing though is that the fork only has two parallel structures handling stiffness and loads of all directions. A rear triangle has two triangular structures, and they are set wider apart so independently of the hub interface, it's much easier to have a laterally stiff rear compared to a fork. Most companies have found out a rear thru-axle doesn't really make things that much stiffer, but make it easier to have a consistent rotor/caliper alignement when removing and putting the wheel back in as QR on some hubs makes a big difference in side to side alignement depending how tight you put the QR and the axle can sit not quite perfectly in the dropouts with QR, something that's physically not possible with thru-axles, so a rear thru-axle is more about making things easier for all consumers than adding stiffness. Plus, it makes more sense to use the same interface front and rear and that's what the whole industry went with, it looks less like a DIY thing to have the same interface front and back as well.
So my opinion is that thru-axles are indeed better and nicer but just that wouldn't be a deciding factor to change a bike IMO. There are many good reasons to change it though.
Only Shimano have direct mount rear derailleurs so frames can't only have DM mounts as stock, otherwise they couldn't be used with SRAM and Campagnolo while all Shimano derailleurs that are direct-mount compatible come with the normal hanger part already installed. Plus, probably 99.9% of consumers don't know about direct mount hangers and couldn't care less when they do.
The EF mounts have no brand and can't be bought, an industrial metal shop machinist in Italy that doesn't really have anything to do with cycling made a bunch for the various Cannondale sponsored teams.