There are many thing that can be done to improve on Hobies designs.
First and foremost they should be looking for ways to improve their mirage drive pockets in the hulls, this is by far their biggest weakness. The entire mirage drive pocket could ( and should) be designed as an inserted injection molded piece inserted into and bolted together after molding, it would be 10 times stronger than their current design (no more mirage drive cracks ever). The unit would look very similar to the insert they now use in their inflatable line of kayaks, the upper flange would bolt onto the lower flange/body (so it can be removed and replaced easily). The mirage drive mechanics would no longer have anything whatsoever to do with hull seal (hobies biggest issue). In reality going to such a design would reduce the cost of all Hobie Mirage kayaks considerably. Since all the mechanicals are in the injection molded piece it would be impossible to ever leak. The opening in the hull itself would be just a flange on the bottom, a flange on the top, and a simple oval thru the hull, no inserts, no fancy rotomolding tricks needed (besides a chilled core maybe). This separates the task of hull seal from the mechanical design aspects completely, making everything 100 times simpler, better yet injection molding is 10 times more accurate than roto-molding so the fits on everything could be much closer vs the loosie goosy design they have now. The best part is, (drum roll) all of their existing kayak molds could easily be retrofitted with this new design. The mirage pocket insert could be common across most of their lines of kayaks further reducing costs. And on the off chance there is a mechanical failure (something breaks in the mirage holder), they don't have to build you a completely new boat, they just send you a new mirage insert via UPS ($10 bucks shipping, or next day air if your in a rush LOL). You basically just slip out the old one and slap in the new unit by tightening 4 stainless bolts ( a 100x cost reduction). All secondary operations within the hull after rotomolding would be eliminated, and setup time prior to roto-molding would be reduced by eliminating those crazy brass inserts that have to be bolted into the mold prior to roto-molding.
Once that problem is solved they can then start thinking about hull materials.
I personally don't think thermoforming would be the answer on Hobies kayak line either. The materials typically used for thermoforming are materials like ABS, and I don't feel are superior to injection molded engineered resins.
First off, I feel Hobie's roto-molding process is pretty darn good just as it is, these days they have very few failures, they have become quite expert at chilled inserts, chilling strategic areas (like the scupper holes), and have their materials down to a science. And they know how to design the hull to take advantage of all the technologies strengths, and design around all of it's weaknesses. If you look at hulls like the Tandem Island hull, it is indeed a technology marvel, an obvious culmination of years and years of hard knocks learning on Hobies part.
These days the material sciences are very mature and they have complete families of plastic resins that chemically bond to each other. If you look at a tooth brush, or an electric drill, or a cell phone these are all great examples of chemically bonded resins. Actually your not limited to two different resins, as we have developed parts with as many as 6 different resins/colors all molded together in one operation. I should know the Swedish company I worked at for 30+ years invented 2 shot technology and held all the patents for it until 1985 (this stuff is pretty much what I've been doing my whole life).
I'm not in the boat business and have no association with Hobie, except as my hobby on weekends, and I like to putze around with my TI, kayaking and sailing is actually a pretty good exercise program for me, as I try to pedal/kayak/sail my TI 15 to 50 miles every weekend year round. I'm actually on my 3rd TI now with way in excess of 5000 pedaling/sailing miles on my TI's to date, with really no issues of any kind, I don't baby my boats and tend to push them more than most would, I consider the design of the boat to be very solid.
Now if I were to want to improve on the design slightly and want for anything else it would be more scratch resistance on the hull body, anyone who has moored at a dock in a marina, or gone over oyster beds and rocky rivers knows what I'm taking about with Hobie kayaks, such things typically scratch my hulls beyond recognition after a while (keep in mind I use the heck out of all my stuff).
My opinion is there is probably a way to improve the hull hardness on some of the higher end Hobie kayaks.
One option would be to spray an initial coat of some harder material into the hull mold bottom prior to rotomolding (like gelcoat). This would be sprayed in similar to the way they spray in gelcoat into fiberglass boat hulls. then spatter spray with fiberglass (like they make fiberglass boat hulls currently). Since you are spraying directly into the lower mold half, the process should be easy and quick, obviously a mold release agent will be needed. Basically you would gelcoat with some heat resistant (exo-thermal epoxy type thermoset material), The spattered fiberglass standing up on the surface is what would mechanically bond to the PE material during the roto-molding process. Once the parting line is cleaned up and the epoxy has setup, the mold is closed and the roto-molding process begins. The hull top and the rest of the boat is then roto-molded (just like they do currently). Once completed the entire completed boat is removed from the mold with a nice fiberglass hard gelcoat type hull bottom with a completely sealed SOT kayak (and happy customers). The water seal itself is provided by the PE roto-molded coating on the inside of the hull, so even if the hard skin gets damaged and cracked by a collision, water seal is maintained by the PE rotomolded inner hull (which can now be much thinner). Of course there is a couple tricks in designing it to insure it all works, but in reality, it should be fairly inexpensive and very reliable. ( Plus you could select two tone colors LOL)
The result would be a hard skinned rotomolded hull (they actually may already be doing something like this on some of their sail boat line already, I'm not familiar with all their stuff). Of course anything you do extra always adds considerable cost.
The second method would be to roto-mold each hull twice (not practical), once with the harder material(higher melt temp (ie... glass filled nylon)), which would be around 1/16-3/32 thick, then finish off with a standard rotomold process using PE, possibly their current material. Of course additives would be required for the chemical bond between the dis-similar resins.
A third process option (and probably the most expensive as well as not practical) would be to injection mold the hull bottom (basically all the high wear areas under the boat) as a thin walled injection molded piece(s) (about 2.5 mm thick) in a durable resin using sequential valve gating similar to the way we make automotive facias (the front and rear of most cars on the market). In the mold design on the inside surface there would be all kinds of protrusions that would create what we call a mechanical bond to the PE material, this way you would get both chemical and mechanical bonding to the PE material. This component would be the pre-mold and pretty much any durable engineered resin could be used (with the proper additive to give it some chemical bonding characteristics to PE). This pre-molded insert which only took about 60 seconds to mold (cycle time) would then be placed into the rotary mold as an insert (similar to how they now put the Hobie IML labels into the mold prior to molding currently), of course the chosen material has to have a higher melt temp than their standard PE. To make things easier they could break it up into 3-4 different parts, basically covering the bow, the stern, and around the mirage drives (or whatever they want to re-enforce). There are several ways to hold the inserts in during rotomolding, either mechanically, using vacuum, or any host of other methods. Since the injection molded resins like GF nylon are much stronger and the injection molding process is much more exact, this would enhance the structural integrity of the entire boat (the shell would be like the frame on a car, actually making the entire boat lighter and stronger, since injection molded engineering resins don't creep and sag like the PE does. A heat conductive ceramic additive might be required to the plastic so it can conduct heat a little better during the roto-molding process (because plastic is naturally an insulator), there are all kinds of these ceramics currently being used in thing like electric motors, armatures, etc.
The thing I like about all the above suggestions is they all completely separate the mechanical design and durability from the water tightness of the boat. for example if one of those hull plates cracks from a dock collision, the boat is still water tight (you still have the PE roto-molded inner area providing your water seal), to repair the crack you could just glue the crack back together or tape over it, because the hard skin or mechanicals have nothing to do with the water seal. To be honest I just don't see any of this happening.
You might be thinking why couldn't they use thermoforming to make the hull bottom (vs injection molding), then roto-mold with that thermoformed hull bottom already in the mold ( I suspect what you were alluding to) using a large thermoformed hull bottom insert. First off most thermoformed materials would be far inferior (ABS for example) to Injection molded plastics, and there would be no means to design in the mechanical bonds needed for the overmolding process via thermoforming, currently I know of no thermoforming materials that have been developed that are chemically compatible to PE (for a chemical bond to the PE plastic). Plus thermoforming is not even in the same realm precision wise to any injection molding process, accuracy wise it's even less accurate than rotomolding. Another big deal about thermoforming is in its name, the plastic is heated up and stretched to thermoform it, you wouldn't be able to thermoform, then rotomold over it (it would melt away, or worse yet shrink back to it's pre thermoformed shape just like the Hobie water bottles do (which are thermoformed) when you put them in the dishwasher.
There are a gazzilion options and ideas out there, all it costs is money to invent and develop them into products.
Hobie is a little stubborn in some ways, and prefer to come up with their own solutions internally, hopefully one of their guys will think of some of this stuff internally someday ( LOL). I think they prefer to learn via hard knocks, and are typically not interested in ideas from outside sources.