Personally I like the Sit In Yak, but if you are doing alot of fishing I would suggest a Sit On Top Yak. I think it is just a matter of preference of which you would want to choose. Rent one of each from an REI or local boat store to make your big decision!
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I wasnt sold on fishing from a kayak until some brothers from the macaw tribe took me out and we came face to face with a Killer Whale (Orca for all you PC) it is something I will remember for the rest of my life. That and the Salmon fish fry at the church. Later
I recently purchased a 2 man pelican top seated blow molded kayak, and let me say its AMAZING! Really the fact it can hold 2 200+ lb guys plus our back packs. It floats about 8 inches out of the water which is awesome because unlike a canoe I spin my body sideways and hang my feet in the water like a bench throw out a 10lb weight i have as an anchor and bungee the ores its great.
I have a sit in and I would like to pass that to my wife (she doesn't do as much fishing) and get a 12' open/sit on yak. I find it hard to fish from the one that I have now.
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Ever try to fish 10ft down in 8ft of water??
SOT all the way! If fishing is its purpose SOT's are hard to argue against.
But, the best thing you can do is test them both out. Locally some retailers allow certain days for testing different models out. I'm sure you could find some retailer near you that would do the same.