SOT is the only way to go, and I mean ONLY way. If you get a sit-in you will be extremely uncomfortable and disappointed. I just sold mine and I'm currently about to buy a brand new one. Old one was 11'5" SOT and it tracked very well - in rivers and on the lake. The longer the yak the easier it will track but harder to transport obviously. SOT are also very hard to flip - couldnt tell you how many strainers I hit and still could not flip it. I would stand up in it casting a fly rod or a cast net and couldn't flip it... You will def not be able to fly fish from a sit inside and getting in and out is a chore in and of itself.
Disclaimer: kayak fishing is the most addictive form of fishing!! They take you places even the best jet cannot go

Not to mention you get a great workout and cant even feel it until the next day - your arms, chest and abs will be ripped before you know it...just another perk of yak fishing I guess

So long story short - get a good sturdy SOT that can take a beating - and make sure it has plenty of storage, if not you can always customize! Also invest in a good paddle it will be well worth it. Winter kayak fishing is awesome and a very dry ride if your paddling technique is good- meaning no freezing water dripping down your paddle. Use scuppers in the winter to plug the bottom of the yak and you should be 100% dry (take them out in summer for a cooling wet float if you like) Have fun with it!