That’s quite a good idea. Have you any experience with kayaks vs pontoons. I’ve read a lot but personal experience is always welcome
I think it is important to consider where and how you will be fishing. With a trolling motor, I am able to use 2 downriggers mounted to either side of the pontoon, which greatly helps the boat tracking straight when I am trolling. I have heard from Kayak users that they need to use 2 downriggers - 1 doesn't work because it wants to tip over. I can use 1 downrigger just fine. I don't use downriggers for trout fishing, but for kokanee (and the Baker Lake sockeye salmon fishery) they are a must. I am considering doing some relatively tame drifts this fall for salmon on a couple of rivers - some people are more adventurous than me, but slow meandering rivers are certainly doable with a pontoon.
For fishing without the motor, I have the choice of rowing or wearing fins like a float tube. Some people mount their seat on an extension so they are higher off the water for casting - I would do this if I was fly-fishing much. That isn't an option with a Kayak, and I don't think kayaks are well suited to fly fishing in general - but please chime in on this one.
Honestly, the pontoon pressure is the least bothersome aspect of owning a pontoon - the biggest pain in the butt is having to completely unload it - take off the motor, battery, downriggers, etc - before loading it on my car. You would have this same problem with a Kayak, plus with most Kayaks you can't use a motor at all. Most of the users of the high-end fishing kayaks I have seen prefer to use a trailer with their kayaks - which defeats the point of getting a car topper to begin with.
And the price - I'm all in for under $1,000 with my pontoon (used), pump, motor, battery, charger, rod holders, downriggers, downrigger balls, and fish finder. The comparable fishing kayaks I have seen are at least $3,000 (US) without the equipment.