Sorry about the delay in replying. Replying got lost in the shuffle.
We normally use hytrel, silicone, or neoprene for the boots. Often changing by the buyer's specifications. The different materials all have their pros and cons. Hytrel is likely what Toyota OEM boots are made of. It's strong, wears well, and is resistant to tears. For the backyard mechanic hytrel can be a difficult material to work with since it doesn't conform as much as silicone or neoprene and at the very least you'll probably need a specialized tool such as an Oetiker Stepless to crimp the band clamps.
Silicone is good with abrasion resistance, is very flexible, and wears well with increased joint angles where self abrading (those really severe joint angles where the convolutions are rubbing on each other while driving down the highway) can kill a neoprene or hytrel boot in a few thousand miles. They are however intolerant of nics, cuts, and punctures. Once the silicone gets damaged it tends to open up in a hurry. Silicone boots are also expensive at nearly $100 per joint (roughly $200 for both joints on a single half shaft).
Neoprene is tolerant of punctures and often will keep working long after a nic or small cut but doesn't have the self abrading resistance of silicone. It's a good material to work with as a DIY'er since the material will accept different clamps and still get a good seal. They also tend to dry out and crack faster than hytrel or silicone. In rough terms maybe 10% - 40% shorter life? Hard to say with all the variables.
So what's the best one? Well it all depends on your preference. I tend to run the hytrel and neoprene on my personal rig. I have near a 2.75” lift up front and tend to need to replace my boots every couple of years depending on mileage or if I do some hard wheeling and break another axle. When the broken axle comes off I replace both the boots as normal maintenance. As far as I know there's no perfect boot, they all are still wear items. In my personal experience the hytrel and the silicone have faired the best but I carry the neoprene boot kits as a spare part on my rig since they are easier to work with in the field.
We don't upgrade the inner joint for a couple of reasons. The inner joint, the tripod, doesn't have the inherent weakness at higher joint angles like the outer joint. The inner joint tends to be weakest if the front suspension is biased too far in the droop direction. Some rigs are set up with coils that are so stiff and/or so much lift that the rig is riding with droop even on a level surface. The more bias to droop in the IFS the more the bearings within the inner joint are pulled to the edge of the cup housing. That's why you often see rigs blow up the inner joint when they are nose up on an obstacle. The front suspension unloads and “lengthens” the half shaft. The bearings are pulled to the edge of the cup where there is less material to support the torque loads.
When it comes to an OEM outer joint, it's actually quite strong at stock ride height when there is virtually no joint angle. It's mainly a problem when the steering is at full turn along with suspension droop. That's when the inner guts of the outer joint start to actually pry on itself. It puts huge pressures on the edge of the cage and race. Often resulting in a cracks that don't show symptoms until later in the trail when the broken pieces have the chance to work themselves into other parts of the joint causing crunching or lockup.
This is why just the outer joint in our axles (and not the inner) are machined with deeper, thicker, and chromoly steel. And why we build them to handle so much more pressure before failure. Depending on how a driver is minding the CV joint angles and wheel speed they are nearly the same strength as the bar and inner joint when they would be at their strongest in a flat ride height. We could machine new inner joints too but the cost would go way up and the overall benefit really isn't there. For example if the inner joint is “bulletproof” you still have the mid bar and the outer bar that can fail. If you upgrade all the components in the half shaft then you move your break point inside the differential. So in the end it's a matter of taking the entire system into consideration and engineering for the overall performance. You'd also be approaching or exceeding the cost of an RCV axle which have a lifetime warranty.
If you break an axle after a year then yes, they are out of warranty and yes the sting of the broken part is going to be real. However you should still get in touch with us since we'd like to try and help out on a case by case basis. This might mean getting you a discount on a replacement or maybe trying to help out in some other way.
As far as some people being unhappy with the necessary evils when it comes to the cost of manufacturing. We understand. Off-roading is an expensive past time. We get it, that it can be frustrating when the difference between getting to have the higher strength part (or not) comes down to the current budget. We'd give them away if we could do so sustainably because we also love the community and the people in it. I can't tell you how often I've run into good people helping out with trash pickup, trail maintenance, and being good stewards of the land in general. They are often off-roaders in built up rigs that dedicate a part of their life to something truly worthy. But until one of us wins the mega millions we're stuck selling them at as low a price we can while still staying in business. Thanks for understanding and for the questions! Let us know if you have more questions.